Microarray Analysis Script for Affymetrix MoGene-1_0-st-v1 using APT (Affymetrix Power Tools) with plier_gcbg normalization and limma. Data already without Probe9 so KO6_4
Install packages only ONCE! if (!requireNamespace(“BiocManager”)) install.packages(“BiocManager”) BiocManager::install(c( “oligo”, “limma”, “pd.mogene.1.0.st.v1”, “mogene10sttranscriptcluster.db”, “AnnotationDbi”, “pheatmap”, “ggplot2”, “ggrepel”, “fgsea”, “gprofiler2”, “topGO”, “org.Mm.eg.db”, “GO.db”, “gtools”, “rmarkdown” )) BiocManager::install(“Rgraphviz”) BiocManager::install(“tidyverse”) Load libraries
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## unionCreating results folders
dir.create("results", showWarnings = FALSE)
dir.create("results/plots", showWarnings = FALSE)
dir.create("results/tables", showWarnings = FALSE)
dir.create("results/report", showWarnings = FALSE)Loading expression data after plier-gcbg normalization with APT
plier_gcbg <- read.table("../after_plier-gcbg_apt.txt", sep = "\t", header = TRUE, stringsAsFactors = FALSE, row.names=1)
head(plier_gcbg)## Probe10_MoGene.1_0.st.v1.CEL Probe1_MoGene.1_0.st.v1.CEL
## 10338001 5214.84368 8551.04834
## 10338002 380.86360 436.23978
## 10338003 1765.73652 3213.52305
## 10338004 925.23751 1801.00505
## 10338005 3.72918 4.86664
## 10338006 6.52560 7.83556
## Probe2_MoGene.1_0.st.v1.CEL Probe3_MoGene.1_0.st.v1.CEL
## 10338001 6906.92956 5808.41827
## 10338002 411.18993 395.80109
## 10338003 2505.77465 1883.42023
## 10338004 1428.19626 1070.28511
## 10338005 4.50069 3.78677
## 10338006 8.78201 6.72858
## Probe4_MoGene.1_0.st.v1.CEL Probe5_MoGene.1_0.st.v1.CEL
## 10338001 5395.24590 7036.96409
## 10338002 403.04392 419.90256
## 10338003 1741.93935 2597.90603
## 10338004 1007.94946 1419.30711
## 10338005 4.12863 3.78353
## 10338006 6.40796 6.60167
## Probe6_MoGene.1_0.st.v1.CEL Probe7_MoGene.1_0.st.v1.CEL
## 10338001 4948.37600 6949.96359
## 10338002 311.14790 478.52343
## 10338003 1649.83037 2554.77039
## 10338004 895.16164 1427.63743
## 10338005 3.41210 4.28293
## 10338006 5.44459 7.51203
## Probe8_MoGene.1_0.st.v1.CEL
## 10338001 6934.13622
## 10338002 455.42734
## 10338003 2525.69117
## 10338004 1295.26136
## 10338005 2.25587
## 10338006 6.03033Removing MoGene.1_0.st.v1 from samples names
colnames(plier_gcbg) <- gsub('_.*CEL', '\\', colnames(plier_gcbg))
colnames(plier_gcbg)## [1] "Probe10" "Probe1" "Probe2" "Probe3" "Probe4" "Probe5" "Probe6"
## [8] "Probe7" "Probe8"Fix sample name order: Probe1 to Probe10 in numeric order
correct_order <- mixedsort(colnames(plier_gcbg))
correct_order## [1] "Probe1" "Probe2" "Probe3" "Probe4" "Probe5" "Probe6" "Probe7"
## [8] "Probe8" "Probe10"plier_gcbg <- plier_gcbg[, correct_order]
head(plier_gcbg)## Probe1 Probe2 Probe3 Probe4 Probe5 Probe6
## 10338001 8551.04834 6906.92956 5808.41827 5395.24590 7036.96409 4948.37600
## 10338002 436.23978 411.18993 395.80109 403.04392 419.90256 311.14790
## 10338003 3213.52305 2505.77465 1883.42023 1741.93935 2597.90603 1649.83037
## 10338004 1801.00505 1428.19626 1070.28511 1007.94946 1419.30711 895.16164
## 10338005 4.86664 4.50069 3.78677 4.12863 3.78353 3.41210
## 10338006 7.83556 8.78201 6.72858 6.40796 6.60167 5.44459
## Probe7 Probe8 Probe10
## 10338001 6949.96359 6934.13622 5214.84368
## 10338002 478.52343 455.42734 380.86360
## 10338003 2554.77039 2525.69117 1765.73652
## 10338004 1427.63743 1295.26136 925.23751
## 10338005 4.28293 2.25587 3.72918
## 10338006 7.51203 6.03033 6.52560Renaming samples from Probe to KO5, KO6 schema
colnames(plier_gcbg) <- c(paste0("KO5_", 1:5), paste0("KO6_", 1:3), "KO6_5")
head(plier_gcbg)## KO5_1 KO5_2 KO5_3 KO5_4 KO5_5 KO6_1
## 10338001 8551.04834 6906.92956 5808.41827 5395.24590 7036.96409 4948.37600
## 10338002 436.23978 411.18993 395.80109 403.04392 419.90256 311.14790
## 10338003 3213.52305 2505.77465 1883.42023 1741.93935 2597.90603 1649.83037
## 10338004 1801.00505 1428.19626 1070.28511 1007.94946 1419.30711 895.16164
## 10338005 4.86664 4.50069 3.78677 4.12863 3.78353 3.41210
## 10338006 7.83556 8.78201 6.72858 6.40796 6.60167 5.44459
## KO6_2 KO6_3 KO6_5
## 10338001 6949.96359 6934.13622 5214.84368
## 10338002 478.52343 455.42734 380.86360
## 10338003 2554.77039 2525.69117 1765.73652
## 10338004 1427.63743 1295.26136 925.23751
## 10338005 4.28293 2.25587 3.72918
## 10338006 7.51203 6.03033 6.52560Logarithmic transformatioon of the data
plier_gcbg_log <- log2(plier_gcbg)
head(plier_gcbg_log)## KO5_1 KO5_2 KO5_3 KO5_4 KO5_5 KO6_1 KO6_2
## 10338001 13.061886 12.753829 12.503930 12.397473 12.780737 12.272739 12.762790
## 10338002 8.768978 8.683661 8.628632 8.654793 8.713911 8.281457 8.902446
## 10338003 11.649940 11.291041 10.879139 10.766479 11.343134 10.688102 11.318978
## 10338004 10.814587 10.479979 10.063779 9.977208 10.470971 9.806004 10.479414
## 10338005 2.282926 2.170146 1.920968 2.045663 1.919733 1.770660 2.098598
## 10338006 2.970036 3.134551 2.750302 2.679865 2.722831 2.444823 2.909203
## KO6_3 KO6_5
## 10338001 12.759500 12.348408
## 10338002 8.831077 8.573131
## 10338003 11.302463 10.786054
## 10338004 10.339028 9.853680
## 10338005 1.173684 1.898858
## 10338006 2.592237 2.706111str(plier_gcbg_log)## 'data.frame': 35556 obs. of 9 variables:
## $ KO5_1: num 13.06 8.77 11.65 10.81 2.28 ...
## $ KO5_2: num 12.75 8.68 11.29 10.48 2.17 ...
## $ KO5_3: num 12.5 8.63 10.88 10.06 1.92 ...
## $ KO5_4: num 12.4 8.65 10.77 9.98 2.05 ...
## $ KO5_5: num 12.78 8.71 11.34 10.47 1.92 ...
## $ KO6_1: num 12.27 8.28 10.69 9.81 1.77 ...
## $ KO6_2: num 12.8 8.9 11.3 10.5 2.1 ...
## $ KO6_3: num 12.76 8.83 11.3 10.34 1.17 ...
## $ KO6_5: num 12.35 8.57 10.79 9.85 1.9 ...Changing values lower than 0 to 0
plier_gcbg_log[plier_gcbg_log < 0] <- 0
min(plier_gcbg_log)## [1] 0max(plier_gcbg_log)## [1] 14.8902Histogram of signal intensities
hist(unlist(plier_gcbg_log), breaks = 100, col = "lightgray",
main = "Histogram intensywności apt (log2)",
xlab = "log2 intensywności")
Checking how many probes with 0 values
plier_gcbg_log_no_zero_rows <- plier_gcbg_log[!apply(plier_gcbg_log == 0, 1, all), ]
str(plier_gcbg_log_no_zero_rows)## 'data.frame': 35552 obs. of 9 variables:
## $ KO5_1: num 13.06 8.77 11.65 10.81 2.28 ...
## $ KO5_2: num 12.75 8.68 11.29 10.48 2.17 ...
## $ KO5_3: num 12.5 8.63 10.88 10.06 1.92 ...
## $ KO5_4: num 12.4 8.65 10.77 9.98 2.05 ...
## $ KO5_5: num 12.78 8.71 11.34 10.47 1.92 ...
## $ KO6_1: num 12.27 8.28 10.69 9.81 1.77 ...
## $ KO6_2: num 12.8 8.9 11.3 10.5 2.1 ...
## $ KO6_3: num 12.76 8.83 11.3 10.34 1.17 ...
## $ KO6_5: num 12.35 8.57 10.79 9.85 1.9 ...plier_gcbg_log_zero_rows <- plier_gcbg_log[apply(plier_gcbg_log == 0, 1, all), ]
str(plier_gcbg_log_zero_rows)## 'data.frame': 4 obs. of 9 variables:
## $ KO5_1: num 0 0 0 0
## $ KO5_2: num 0 0 0 0
## $ KO5_3: num 0 0 0 0
## $ KO5_4: num 0 0 0 0
## $ KO5_5: num 0 0 0 0
## $ KO6_1: num 0 0 0 0
## $ KO6_2: num 0 0 0 0
## $ KO6_3: num 0 0 0 0
## $ KO6_5: num 0 0 0 0plier_gcbg_log_no_any_zeros <- plier_gcbg_log[!apply(plier_gcbg_log == 0, 1, any), ]
str(plier_gcbg_log_no_any_zeros)## 'data.frame': 35214 obs. of 9 variables:
## $ KO5_1: num 13.06 8.77 11.65 10.81 2.28 ...
## $ KO5_2: num 12.75 8.68 11.29 10.48 2.17 ...
## $ KO5_3: num 12.5 8.63 10.88 10.06 1.92 ...
## $ KO5_4: num 12.4 8.65 10.77 9.98 2.05 ...
## $ KO5_5: num 12.78 8.71 11.34 10.47 1.92 ...
## $ KO6_1: num 12.27 8.28 10.69 9.81 1.77 ...
## $ KO6_2: num 12.8 8.9 11.3 10.5 2.1 ...
## $ KO6_3: num 12.76 8.83 11.3 10.34 1.17 ...
## $ KO6_5: num 12.35 8.57 10.79 9.85 1.9 ...plier_gcbg_log_any_zeros <- plier_gcbg_log[apply(plier_gcbg_log == 0, 1, any), ]
str(plier_gcbg_log_any_zeros)## 'data.frame': 342 obs. of 9 variables:
## $ KO5_1: num 0 0 3.86 3.12 0 ...
## $ KO5_2: num 1.79 2.29 0 4.41 2.24 ...
## $ KO5_3: num 1.558 0.677 0.783 0.286 0 ...
## $ KO5_4: num 0.209 1.175 2.732 1.8 0 ...
## $ KO5_5: num 0 0 2.08 0 2.25 ...
## $ KO6_1: num 0.724 1.037 1.034 3.503 0 ...
## $ KO6_2: num 1.24 0.72 3.31 1.97 2.9 ...
## $ KO6_3: num 0 0 0.691 3.993 0 ...
## $ KO6_5: num 0.32 0 0.549 2.749 0 ...min(plier_gcbg_log_any_zeros)## [1] 0max(plier_gcbg_log_any_zeros)## [1] 10.67655Histogram of signal intensities of probes with any zero value
hist(unlist(plier_gcbg_log_any_zeros), breaks = 100, col = "lightgray",
main = "Histogram intensywności apt (log2) any0",
xlab = "log2 intensywności")
Boxplot of probes with any zero value
boxplot(plier_gcbg_log_any_zeros, las = 2, main = "Boxplot po normalizacji (RMA) all", col = "lightblue")
Removing probes with zero value in any sample
plier_gcbg_log <- plier_gcbg_log_no_any_zerosBoxplot all rows
boxplot(plier_gcbg_log, las = 2, main = "Boxplot po normalizacji (RMA) noany0", col = "lightblue")
PCA with probes without zeros in any sample
group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
pca <- prcomp(t(plier_gcbg_log))
group_colors <- ifelse(group == "KO5", "blue", "red")
plot(pca$x[,1:2], col = group_colors, pch = 19,
main = "PCA after APT any0", xlab = "PC1", ylab = "PC2")
text(pca$x[,1], pca$x[,2], labels = colnames(plier_gcbg), pos = 3, cex = 0.8)
legend("topright", legend = levels(group), col = c("blue", "red"), pch = 19)
Correlation between samples
cor_matrix <- cor(plier_gcbg_log)
pheatmap(cor_matrix, main = "Korelacja między próbkami")
Samples dendrogram
sample_distF <- dist(t(plier_gcbg_log))
hc <- hclust(sample_distF)
plot(hc, labels = colnames(plier_gcbg), main = "Sample clustering (hierarchical)", xlab = "", sub = "")
Median expression per sample
mediansF <- apply(plier_gcbg_log, 2, median)
barplot(mediansF, names.arg = colnames(plier_gcbg), las = 2,
col = group_colors, main = "Median expression per sample")
Calculating variation of all genes
varsF <- apply(plier_gcbg_log, 1, var)Heatmap expresison of 100 most variable genes
top_var_genesF <- names(sort(varsF, decreasing = TRUE))[1:100]
expr_topvarF <- plier_gcbg_log[top_var_genesF, ]
group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(expr_topvarF)
pheatmap(expr_topvarF, scale = "row",
annotation_col = annotation_col,
show_rownames = FALSE,
main = "Heatmap of top 100 variable genes")
Heatmap expresison of 500 most variable genes
top_var_genesF <- names(sort(varsF, decreasing = TRUE))[1:500]
expr_topvarF <- plier_gcbg_log[top_var_genesF, ]
group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(expr_topvarF)
pheatmap(expr_topvarF, scale = "row",
annotation_col = annotation_col,
show_rownames = FALSE,
main = "Heatmap of top 500 variable genes")
Heatmap expresison of 1000 most variable genes
top_var_genesF <- names(sort(varsF, decreasing = TRUE))[1:1000]
expr_topvarF <- plier_gcbg_log[top_var_genesF, ]
group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(expr_topvarF)
pheatmap(expr_topvarF, scale = "row",
annotation_col = annotation_col,
show_rownames = FALSE,
main = "Heatmap of top 1000 variable genes")
Euclidan distance between samples
sample_distF <- dist(t(plier_gcbg_log))
sample_dist_matF <- as.matrix(sample_distF)
pheatmap(sample_dist_matF, main = "Sample-to-sample Euclidean distance")
Checking knockout, stable and backgroud genes expression Loading oryginal annotation from mogene10sttranscriptcluster.db
annot_old_exprsF <- select(mogene10sttranscriptcluster.db,
keys = rownames(plier_gcbg_log),
columns = c("SYMBOL"),
keytype = "PROBEID")## 'select()' returned 1:many mapping between keys and columnshead(annot_old_exprsF)## PROBEID SYMBOL
## 1 10338001 <NA>
## 2 10338002 <NA>
## 3 10338003 <NA>
## 4 10338004 <NA>
## 5 10338005 <NA>
## 6 10338006 <NA>str(annot_old_exprsF)## 'data.frame': 46425 obs. of 2 variables:
## $ PROBEID: chr "10338001" "10338002" "10338003" "10338004" ...
## $ SYMBOL : chr NA NA NA NA ...Merging original annotation with expression matrix by ProbeID
exprsF_annot_old <- merge(plier_gcbg_log, annot_old_exprsF, by.x = "row.names", by.y = "PROBEID")Renaming rownames columnn to ProbeID
colnames(exprsF_annot_old)[1] <- "ProbeID"
head(exprsF_annot_old)## ProbeID KO5_1 KO5_2 KO5_3 KO5_4 KO5_5 KO6_1
## 1 10338001 13.061886 12.753829 12.503930 12.397473 12.780737 12.272739
## 2 10338002 8.768978 8.683661 8.628632 8.654793 8.713911 8.281457
## 3 10338003 11.649940 11.291041 10.879139 10.766479 11.343134 10.688102
## 4 10338004 10.814587 10.479979 10.063779 9.977208 10.470971 9.806004
## 5 10338005 2.282926 2.170146 1.920968 2.045663 1.919733 1.770660
## 6 10338006 2.970036 3.134551 2.750302 2.679865 2.722831 2.444823
## KO6_2 KO6_3 KO6_5 SYMBOL
## 1 12.762790 12.759500 12.348408 <NA>
## 2 8.902446 8.831077 8.573131 <NA>
## 3 11.318978 11.302463 10.786054 <NA>
## 4 10.479414 10.339028 9.853680 <NA>
## 5 2.098598 1.173684 1.898858 <NA>
## 6 2.909203 2.592237 2.706111 <NA>str(exprsF_annot_old)## 'data.frame': 46425 obs. of 11 variables:
## $ ProbeID: chr "10338001" "10338002" "10338003" "10338004" ...
## $ KO5_1 : num 13.06 8.77 11.65 10.81 2.28 ...
## $ KO5_2 : num 12.75 8.68 11.29 10.48 2.17 ...
## $ KO5_3 : num 12.5 8.63 10.88 10.06 1.92 ...
## $ KO5_4 : num 12.4 8.65 10.77 9.98 2.05 ...
## $ KO5_5 : num 12.78 8.71 11.34 10.47 1.92 ...
## $ KO6_1 : num 12.27 8.28 10.69 9.81 1.77 ...
## $ KO6_2 : num 12.8 8.9 11.3 10.5 2.1 ...
## $ KO6_3 : num 12.76 8.83 11.3 10.34 1.17 ...
## $ KO6_5 : num 12.35 8.57 10.79 9.85 1.9 ...
## $ SYMBOL : chr NA NA NA NA ...Loading Knockout genes
genes_of_interest <- c("Acr", "Tnp2", "H1f6", "Spmap2", "Creb3l4", "Tex22")Creating a subset table with genes of interest
subset_genes_table <- exprsF_annot_old[exprsF_annot_old$SYMBOL %in% genes_of_interest, ]
subset_genes_table_unique <- subset_genes_table[!duplicated(subset_genes_table$SYMBOL), ]Making expression plot of knockout genes
df_long <- subset_genes_table_unique %>%
pivot_longer(cols = starts_with("KO"),
names_to = "Sample",
values_to = "Expression") %>%
mutate(Group = ifelse(grepl("KO5", Sample), "KO5", "KO6"))
ala <- ggplot(df_long, aes(x = Sample, y = Expression, group = SYMBOL, color = SYMBOL)) +
geom_line(size = 1) +
geom_point(size = 2) +
theme_minimal() +
labs(title = "Ekspresja genów w próbkach KO5 i KO6", y = "log2(Expression)", x = "") +
theme(axis.text.x = element_text(angle = 45, hjust = 1))## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.ggsave("results/plots/Knockout_genes_expression_plot_apt.jpg", ala)## Saving 7 x 5 in imageala
write.csv(subset_genes_table, "results/tables/Knockout_genes_table_apt.csv", row.names = FALSE)Loading reference genes for testis plus CcDS33 and Pxt1
genes_of_interest1 <- c("Ccdc33", "Pxt1", "Gapdh", "Actb", "Hprt", "Ppia", "Polr2a", "Rpl13a", "Ywhaz", "Tbp", "18srRNA", "Sdha")Creating a subset table with genes of interest
subset_genes_table1 <- exprsF_annot_old[exprsF_annot_old$SYMBOL %in% genes_of_interest1, ]
subset_genes_table_unique1 <- subset_genes_table1[!duplicated(subset_genes_table1$SYMBOL), ]Making expresison plot
df_long <- subset_genes_table_unique1 %>%
pivot_longer(cols = starts_with("KO"),
names_to = "Sample",
values_to = "Expression") %>%
mutate(Group = ifelse(grepl("KO5", Sample), "KO5", "KO6"))
ala <- ggplot(df_long, aes(x = Sample, y = Expression, group = SYMBOL, color = SYMBOL)) +
geom_line(size = 1) +
geom_point(size = 2) +
theme_minimal() +
labs(title = "Ekspresja genów w próbkach KO5 i KO6", y = "log2(Expression)", x = "") +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
ggsave("results/plots/reference_genes_testis_apt.jpg", ala)## Saving 7 x 5 in imageala
write.csv(subset_genes_table1, "results/tables/subset_genes_table_apt1.csv", row.names = FALSE)Loading background probes
background_probes <- read.table("../bcg.probes", header = FALSE, stringsAsFactors = FALSE)Renaming rownames column to ProbeID
colnames(background_probes) <- "PROBEID"
head(exprsF_annot_old)## ProbeID KO5_1 KO5_2 KO5_3 KO5_4 KO5_5 KO6_1
## 1 10338001 13.061886 12.753829 12.503930 12.397473 12.780737 12.272739
## 2 10338002 8.768978 8.683661 8.628632 8.654793 8.713911 8.281457
## 3 10338003 11.649940 11.291041 10.879139 10.766479 11.343134 10.688102
## 4 10338004 10.814587 10.479979 10.063779 9.977208 10.470971 9.806004
## 5 10338005 2.282926 2.170146 1.920968 2.045663 1.919733 1.770660
## 6 10338006 2.970036 3.134551 2.750302 2.679865 2.722831 2.444823
## KO6_2 KO6_3 KO6_5 SYMBOL
## 1 12.762790 12.759500 12.348408 <NA>
## 2 8.902446 8.831077 8.573131 <NA>
## 3 11.318978 11.302463 10.786054 <NA>
## 4 10.479414 10.339028 9.853680 <NA>
## 5 2.098598 1.173684 1.898858 <NA>
## 6 2.909203 2.592237 2.706111 <NA>Creating a subset table with background probes
subset_bcg_table <- exprsF_annot_old[exprsF_annot_old$ProbeID %in% background_probes$PROBEID, ]
df_long <- subset_bcg_table %>%
pivot_longer(cols = starts_with("KO"),
names_to = "Sample",
values_to = "Expression") %>%
mutate(Group = ifelse(grepl("KO5", Sample), "KO5", "KO6"))
ala <- ggplot(df_long, aes(x = Sample, y = Expression, group = ProbeID, color = ProbeID)) +
geom_line(size = 1) +
geom_point(size = 2) +
theme_minimal() +
labs(title = "Ekspresja sond tła w próbkach KO5 i KO6", y = "log2(Expression)", x = "") +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
ggsave("results/plots/BckgProbesets_apt.jpg", ala)## Saving 7 x 5 in imageala
write.csv(subset_genes_table1, "results/tables/BckProbes_apt.csv", row.names = FALSE)Checking probesests by variation and expression Calculating variation and mean expression per probeset
gene_var <- apply(plier_gcbg_log, 1, var)
gene_mean <- rowMeans(plier_gcbg_log)Defining low and high variation threshlods
low_var_genes <- which(gene_var <= 0.01)
high_var_genes <- which(gene_var > 0.01)
length(low_var_genes)## [1] 5055length(high_var_genes)## [1] 30159Randomly get 100 probesets with low and high variation
set.seed(42) #' dla powtarzalności
low_sample <- sample(low_var_genes, 100)
high_sample <- sample(high_var_genes, 100)Plotting expression of low and high variation probes
df_long_var <- bind_rows(
plier_gcbg_log[low_sample, ] %>%
as.data.frame() %>%
mutate(VarGroup = "LowVar", ProbeID = rownames(.)),
plier_gcbg_log[high_sample, ] %>%
as.data.frame() %>%
mutate(VarGroup = "HighVar", ProbeID = rownames(.))
) %>%
pivot_longer(cols = starts_with("KO"),
names_to = "Sample",
values_to = "Expression") %>%
mutate(Group = ifelse(grepl("KO5", Sample), "KO5", "KO6"))
p_lines <- ggplot(df_long_var, aes(x = Sample, y = Expression, group = ProbeID)) +
geom_line(aes(color = Group), alpha = 0.4) +
facet_wrap(~VarGroup, scales = "free_y") +
theme_minimal() +
labs(title = "Ekspresja każdej sondy (LowVar / HighVar) w KO5 vs KO6", x = "", y = "log2(Expression)") +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_color_manual(values = c("KO5" = "blue", "KO6" = "red"))
ggsave("results/plots/Variationwise_expression_Probes_KO5vsKO6_apt.jpg", p_lines, width = 10, height = 6)
p_lines
How many high variable genes has expression higher than:
for (i in 2:10) {
print(paste("High variable probesest with expression higher than", i," : ", sum(gene_mean[high_var_genes] >= i)))
}## [1] "High variable probesest with expression higher than 2 : 30139"
## [1] "High variable probesest with expression higher than 3 : 30080"
## [1] "High variable probesest with expression higher than 4 : 29868"
## [1] "High variable probesest with expression higher than 5 : 29223"
## [1] "High variable probesest with expression higher than 6 : 27585"
## [1] "High variable probesest with expression higher than 7 : 23797"
## [1] "High variable probesest with expression higher than 8 : 16932"
## [1] "High variable probesest with expression higher than 9 : 10604"
## [1] "High variable probesest with expression higher than 10 : 6036"Filtering based on variantion and expression higher than threshold in at leat one of the compared groups Separating columns of comparisons groups
ko5_cols <- grep("^KO5", colnames(plier_gcbg_log))
ko6_cols <- grep("^KO6", colnames(plier_gcbg_log))Calculating mean expresison per group
ko5_mean <- rowMeans(plier_gcbg_log[, ko5_cols])
ko6_mean <- rowMeans(plier_gcbg_log[, ko6_cols])Calculating variation per group
ko5_var <- apply(plier_gcbg_log[, ko5_cols], 1, var)
ko6_var <- apply(plier_gcbg_log[, ko6_cols], 1, var)Setting thresholds Threshold of 8 instead of 10 was decideded by looking at expression values after plier_gcbg normalization by Affymetrix Power Toools, which makes the normalization using background antigenomic probes on the chip (abs(ko5_mean - ko6_mean) >= .5) & #’ I am not adding this threshiold of expression difference beteen groups
keep <- ((ko5_mean >= 8) | (ko6_mean >= 8)) &
((ko5_var > 0.01) | (ko6_var > 0.01))Filtering by thresholds
plier_gcbg_log_filtered <- plier_gcbg_log[keep, ]How many left
str(plier_gcbg_log_filtered)## 'data.frame': 17883 obs. of 9 variables:
## $ KO5_1: num 13.06 8.77 11.65 10.81 9.98 ...
## $ KO5_2: num 12.75 8.68 11.29 10.48 9.96 ...
## $ KO5_3: num 12.5 8.63 10.88 10.06 9.69 ...
## $ KO5_4: num 12.4 8.65 10.77 9.98 9.69 ...
## $ KO5_5: num 12.78 8.71 11.34 10.47 10.09 ...
## $ KO6_1: num 12.27 8.28 10.69 9.81 9.51 ...
## $ KO6_2: num 12.8 8.9 11.3 10.5 10 ...
## $ KO6_3: num 12.76 8.83 11.3 10.34 9.9 ...
## $ KO6_5: num 12.35 8.57 10.79 9.85 9.41 ...DE Analysis
group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
group_levels <- levels(group)
group_levels## [1] "KO5" "KO6"design <- model.matrix(~ group)
design## (Intercept) groupKO6
## 1 1 0
## 2 1 0
## 3 1 0
## 4 1 0
## 5 1 0
## 6 1 1
## 7 1 1
## 8 1 1
## 9 1 1
## attr(,"assign")
## [1] 0 1
## attr(,"contrasts")
## attr(,"contrasts")$group
## [1] "contr.treatment"fitF <- lmFit(plier_gcbg_log_filtered, design)
fitF <- eBayes(fitF)Histogram of Mean expressions
hist(fitF$Amean)
plotSA(fitF)
DE results table
resultsF <- topTable(fitF, coef = 2, number = Inf, confint = TRUE)
write.csv(resultsF, "results/tables/results_apt.csv", row.names = FALSE)
head(resultsF)## logFC CI.L CI.R AveExpr t P.Value
## 10389130 -4.288114 -4.556269 -4.019959 8.741076 -34.42180 1.565020e-14
## 10542414 3.703390 3.465927 3.940852 8.645955 33.57049 2.185547e-14
## 10398966 -4.106109 -4.456084 -3.756133 8.843426 -25.25495 9.578656e-13
## 10375121 2.172477 1.959804 2.385150 9.614721 21.98853 5.945455e-12
## 10375123 2.086027 1.879303 2.292752 9.589559 21.72110 6.982184e-12
## 10522127 1.334423 1.071793 1.597054 8.170186 10.93710 4.423838e-08
## adj.P.Val B
## 10389130 1.954207e-10 17.082041
## 10542414 1.954207e-10 16.980163
## 10398966 5.709837e-09 15.556675
## 10375121 2.497248e-08 14.676819
## 10375123 2.497248e-08 14.593079
## 10522127 1.318525e-04 8.582618str(resultsF)## 'data.frame': 17883 obs. of 8 variables:
## $ logFC : num -4.29 3.7 -4.11 2.17 2.09 ...
## $ CI.L : num -4.56 3.47 -4.46 1.96 1.88 ...
## $ CI.R : num -4.02 3.94 -3.76 2.39 2.29 ...
## $ AveExpr : num 8.74 8.65 8.84 9.61 9.59 ...
## $ t : num -34.4 33.6 -25.3 22 21.7 ...
## $ P.Value : num 1.57e-14 2.19e-14 9.58e-13 5.95e-12 6.98e-12 ...
## $ adj.P.Val: num 1.95e-10 1.95e-10 5.71e-09 2.50e-08 2.50e-08 ...
## $ B : num 17.1 17 15.6 14.7 14.6 ...Adnotation with Original mogene10sttranscriptcluster.db Loading Original Annotation
annot_old1 <- select(mogene10sttranscriptcluster.db,
keys = rownames(resultsF),
columns = c("SYMBOL", "ENSEMBL"),
keytype = "PROBEID")## 'select()' returned 1:many mapping between keys and columnsstr(annot_old1)## 'data.frame': 24881 obs. of 3 variables:
## $ PROBEID: chr "10389130" "10542414" "10398966" "10375121" ...
## $ SYMBOL : chr "Slfn5os" "Ptpro" "Tex22" NA ...
## $ ENSEMBL: chr "ENSMUSG00000086327" "ENSMUSG00000030223" "ENSMUSG00000012211" NA ...head(annot_old1)## PROBEID SYMBOL ENSEMBL
## 1 10389130 Slfn5os ENSMUSG00000086327
## 2 10542414 Ptpro ENSMUSG00000030223
## 3 10398966 Tex22 ENSMUSG00000012211
## 4 10375121 <NA> <NA>
## 5 10375123 <NA> <NA>
## 6 10522127 Klb ENSMUSG00000029195number of probes with more than one adnotation
sum(duplicated(annot_old1$PROBEID))## [1] 6998Merging DE results with Original Annotation table
results_annot_old1 <- merge(resultsF, annot_old1, by.x = "row.names", by.y = "PROBEID")
head(results_annot_old1)## Row.names logFC CI.L CI.R AveExpr t P.Value
## 1 10338001 -0.16371142 -0.4764832 0.1490603 12.626810 -1.1266915 0.2795288
## 2 10338002 -0.04296735 -0.2936639 0.2077292 8.670898 -0.3689299 0.7179093
## 3 10338003 -0.16204730 -0.5575564 0.2334618 11.113925 -0.8819397 0.3932628
## 4 10338004 -0.24177318 -0.6292171 0.1456707 10.253850 -1.3432377 0.2013710
## 5 10338009 -0.17007889 -0.4648539 0.1246962 9.806877 -1.2419762 0.2354179
## 6 10338016 -0.09271588 -0.3339338 0.1485020 9.377283 -0.8273671 0.4224330
## adj.P.Val B SYMBOL ENSEMBL
## 1 0.5265948 -5.746507 <NA> <NA>
## 2 0.8567482 -6.308196 <NA> <NA>
## 3 0.6260209 -5.984502 <NA> <NA>
## 4 0.4461390 -5.496695 <NA> <NA>
## 5 0.4818564 -5.617819 <NA> <NA>
## 6 0.6493075 -6.030613 <NA> <NA>str(results_annot_old1)## 'data.frame': 24881 obs. of 11 variables:
## $ Row.names: chr "10338001" "10338002" "10338003" "10338004" ...
## $ logFC : num -0.164 -0.043 -0.162 -0.242 -0.17 ...
## $ CI.L : num -0.476 -0.294 -0.558 -0.629 -0.465 ...
## $ CI.R : num 0.149 0.208 0.233 0.146 0.125 ...
## $ AveExpr : num 12.63 8.67 11.11 10.25 9.81 ...
## $ t : num -1.127 -0.369 -0.882 -1.343 -1.242 ...
## $ P.Value : num 0.28 0.718 0.393 0.201 0.235 ...
## $ adj.P.Val: num 0.527 0.857 0.626 0.446 0.482 ...
## $ B : num -5.75 -6.31 -5.98 -5.5 -5.62 ...
## $ SYMBOL : chr NA NA NA NA ...
## $ ENSEMBL : chr NA NA NA NA ...naming rownames column with ProbeID
colnames(results_annot_old1)[1] <- "ProbeID"filtering out rows without SYMBOL or ENSEMBL
results_annot_old1 <- results_annot_old1 %>%
filter(
(!is.na(SYMBOL) & SYMBOL != "") |
(!is.na(ENSEMBL) & ENSEMBL != "")
)
str(results_annot_old1)## 'data.frame': 20188 obs. of 11 variables:
## $ ProbeID : chr "10344624" "10344633" "10344637" "10344658" ...
## $ logFC : num -0.118 -0.0337 -0.0848 -0.0362 -0.2313 ...
## $ CI.L : num -0.292 -0.221 -0.275 -0.227 -0.416 ...
## $ CI.R : num 0.0565 0.1536 0.1052 0.1549 -0.0465 ...
## $ AveExpr : num 12.08 11.36 11.12 12.33 9.78 ...
## $ t : num -1.455 -0.387 -0.961 -0.408 -2.695 ...
## $ P.Value : num 0.1685 0.7048 0.3536 0.6898 0.0179 ...
## $ adj.P.Val: num 0.411 0.848 0.595 0.84 0.168 ...
## $ B : num -5.35 -6.3 -5.91 -6.29 -3.37 ...
## $ SYMBOL : chr "Lypla1" "Tcea1" "Atp6v1h" "Rb1cc1" ...
## $ ENSEMBL : chr "ENSMUSG00000025903" "ENSMUSG00000033813" "ENSMUSG00000033793" "ENSMUSG00000025907" ...head(results_annot_old1)## ProbeID logFC CI.L CI.R AveExpr t P.Value
## 1 10344624 -0.11796296 -0.2924560 0.05653009 12.078768 -1.4551948 0.16850306
## 2 10344633 -0.03365629 -0.2208716 0.15355899 11.362263 -0.3869711 0.70481722
## 3 10344637 -0.08481478 -0.2748344 0.10520485 11.123007 -0.9607860 0.35357609
## 4 10344658 -0.03621075 -0.2273545 0.15493297 12.333149 -0.4077848 0.68983356
## 5 10344707 -0.23134278 -0.4161381 -0.04654740 9.779085 -2.6947498 0.01790379
## 6 10344713 -0.32060534 -0.6176199 -0.02359074 9.898482 -2.3235207 0.03636137
## adj.P.Val B SYMBOL ENSEMBL
## 1 0.4106491 -5.354516 Lypla1 ENSMUSG00000025903
## 2 0.8480457 -6.301155 Tcea1 ENSMUSG00000033813
## 3 0.5947829 -5.913296 Atp6v1h ENSMUSG00000033793
## 4 0.8395928 -6.292624 Rb1cc1 ENSMUSG00000025907
## 5 0.1684237 -3.368097 Pcmtd1 ENSMUSG00000051285
## 6 0.2162651 -4.021586 Ahcyl ENSMUSG00000048087write.csv(results_annot_old1, "results/tables/diff_expr_resultsF_oryg_annot.csv", row.names = FALSE)Checking uniquness of the Probes and Genes How many ENSEMBL with more than 1 Probe
symbol_probe_counts <- results_annot_old1 %>%
group_by(ENSEMBL) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 1456How many SYMBOL with more than 1 Probe
symbol_probe_counts <- results_annot_old1 %>%
group_by(SYMBOL) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 1534How many Probes mapping to more than 1 ENSEMBL
probe_symbol_counts <- results_annot_old1 %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(ENSEMBL)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) ## [1] 1095How many Probes mapping to more than 1 SYMBOL
probe_symbol_counts <- results_annot_old1 %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(SYMBOL)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) ## [1] 1089Solving problems with Non unique Genes and Probes List of ProbeIDs with more than one gene based on SYMBOL or ENSEMBL
conflict_ids <- results_annot_old1 %>%
group_by(ProbeID) %>%
filter(n_distinct(SYMBOL) > 1 | n_distinct(ENSEMBL) > 1) %>%
pull(ProbeID) %>%
unique()
length(conflict_ids)## [1] 1112Removal of ProbeIDs with nonunique Genes If ProbeID with just 1 row - stays If SYMBOLs with the same ENSEMBL have common core, randomly choose one row. Other way remove rows.
filtered_results_old1 <- results_annot_old1 %>%
group_by(ProbeID) %>%
group_modify(~ {
subdf <- .x
if (nrow(subdf) == 1) return(subdf)
unique_symbols <- unique(subdf$SYMBOL)
unique_symbols <- unique_symbols[!is.na(unique_symbols) & unique_symbols != ""]
unique_ensembls <- unique(subdf$ENSEMBL)
unique_ensembls <- unique_ensembls[!is.na(unique_ensembls) & unique_ensembls != ""]
roots <- stringr::str_extract(unique_symbols, "^[A-Za-z]{3,}")
roots <- na.omit(roots)
common_root <- length(roots) > 0 && length(unique(roots)) == 1
single_valid_ensembl <- length(unique_ensembls) == 1
if (common_root && single_valid_ensembl) {
return(subdf[sample(nrow(subdf), 1), ])
} else {
return(subdf[0, ])
}
}) %>%
ungroup()
str(filtered_results_old1)## tibble [12,185 × 11] (S3: tbl_df/tbl/data.frame)
## $ ProbeID : chr [1:12185] "10344624" "10344633" "10344637" "10344658" ...
## $ logFC : num [1:12185] -0.118 -0.0337 -0.0848 -0.0362 -0.2313 ...
## $ CI.L : num [1:12185] -0.292 -0.221 -0.275 -0.227 -0.416 ...
## $ CI.R : num [1:12185] 0.0565 0.1536 0.1052 0.1549 -0.0465 ...
## $ AveExpr : num [1:12185] 12.08 11.36 11.12 12.33 9.78 ...
## $ t : num [1:12185] -1.455 -0.387 -0.961 -0.408 -2.695 ...
## $ P.Value : num [1:12185] 0.1685 0.7048 0.3536 0.6898 0.0179 ...
## $ adj.P.Val: num [1:12185] 0.411 0.848 0.595 0.84 0.168 ...
## $ B : num [1:12185] -5.35 -6.3 -5.91 -6.29 -3.37 ...
## $ SYMBOL : chr [1:12185] "Lypla1" "Tcea1" "Atp6v1h" "Rb1cc1" ...
## $ ENSEMBL : chr [1:12185] "ENSMUSG00000025903" "ENSMUSG00000033813" "ENSMUSG00000033793" "ENSMUSG00000025907" ...Make pairs by SYMBOL
symbol_edges <- filtered_results_old1 %>%
filter(!is.na(SYMBOL) & SYMBOL != "") %>%
group_by(SYMBOL) %>%
filter(n() > 1) %>%
reframe(pairs = combn(ProbeID, 2, simplify = FALSE))
nrow(symbol_edges)## [1] 3964Make pairs by ENSEMBL
ensembl_edges <- filtered_results_old1 %>%
filter(!is.na(ENSEMBL) & ENSEMBL != "") %>%
group_by(ENSEMBL) %>%
filter(n() > 1) %>%
reframe(pairs = combn(ProbeID, 2, simplify = FALSE))
nrow(ensembl_edges)## [1] 3913Connecting pairs lists
edges <- bind_rows(symbol_edges, ensembl_edges) %>%
pull(pairs)
length(edges)## [1] 7877Making data.frame
edge_df <- do.call(rbind, lapply(edges, function(x) data.frame(from = x[1], to = x[2])))
str(edge_df)## 'data.frame': 7877 obs. of 2 variables:
## $ from: chr "10394783" "10502417" "10394805" "10425651" ...
## $ to : chr "10394786" "10552622" "10394833" "10425653" ...Creating graph
g <- graph_from_data_frame(edge_df, directed = FALSE)
clusters <- components(g)Annotatioing genes with clusters
cluster_map <- data.frame(ProbeID = names(clusters$membership),
gene_cluster = paste0("C", clusters$membership))Joining clusters with z ProbeId, ENsembl, Symbol i DE
filtered_results_old1_clustered <- filtered_results_old1 %>%
left_join(cluster_map, by = "ProbeID") %>%
mutate(gene_cluster = ifelse(is.na(gene_cluster), paste0("single_", ProbeID), gene_cluster))Choose bedt ProbeiD by FDR or LogFC
results_genes_unique_old1 <- filtered_results_old1_clustered %>%
group_by(gene_cluster) %>%
arrange(adj.P.Val, desc(abs(logFC))) %>%
summarise(best_row = list(first(cur_data())), .groups = "drop") %>%
unnest(best_row) %>%
dplyr::select(-gene_cluster) %>%
as.data.frame()## Warning: There was 1 warning in `summarise()`.
## ℹ In argument: `best_row = list(first(cur_data()))`.
## ℹ In group 1: `gene_cluster = "C1"`.
## Caused by warning:
## ! `cur_data()` was deprecated in dplyr 1.1.0.
## ℹ Please use `pick()` instead.head(results_genes_unique_old1)## ProbeID logFC CI.L CI.R AveExpr t P.Value
## 1 10394783 0.41175139 -0.05185455 0.87535733 9.463494 1.9117878 0.077393739
## 2 10531181 0.16846035 -0.02967207 0.36659276 8.059947 1.8301882 0.089414178
## 3 10587627 0.03612688 -0.16509952 0.23735329 10.218247 0.3864552 0.705190280
## 4 10462136 -0.42016703 -0.65071096 -0.18962309 10.383647 -3.9230321 0.001637431
## 5 10448559 0.21358447 -0.09590773 0.52307666 7.927709 1.4855031 0.160416411
## 6 10586250 -0.19381215 -0.41163701 0.02401272 8.952325 -1.9152573 0.076916655
## adj.P.Val B SYMBOL ENSEMBL
## 1 0.29175480 -4.697095 1700030C10Rik ENSMUSG00000099759
## 2 0.31236447 -4.822682 Adamts3 ENSMUSG00000043635
## 3 0.84827329 -6.301361 Cyb5r4 ENSMUSG00000032872
## 4 0.06313255 -1.094365 Cycs ENSMUSG00000063694
## 5 0.40060420 -5.314608 D330041H03Rik ENSMUSG00000073437
## 6 0.29074203 -4.691687 Dennd4a ENSMUSG00000053641str(results_genes_unique_old1)## 'data.frame': 11107 obs. of 11 variables:
## $ ProbeID : chr "10394783" "10531181" "10587627" "10462136" ...
## $ logFC : num 0.4118 0.1685 0.0361 -0.4202 0.2136 ...
## $ CI.L : num -0.0519 -0.0297 -0.1651 -0.6507 -0.0959 ...
## $ CI.R : num 0.875 0.367 0.237 -0.19 0.523 ...
## $ AveExpr : num 9.46 8.06 10.22 10.38 7.93 ...
## $ t : num 1.912 1.83 0.386 -3.923 1.486 ...
## $ P.Value : num 0.07739 0.08941 0.70519 0.00164 0.16042 ...
## $ adj.P.Val: num 0.2918 0.3124 0.8483 0.0631 0.4006 ...
## $ B : num -4.7 -4.82 -6.3 -1.09 -5.31 ...
## $ SYMBOL : chr "1700030C10Rik" "Adamts3" "Cyb5r4" "Cycs" ...
## $ ENSEMBL : chr "ENSMUSG00000099759" "ENSMUSG00000043635" "ENSMUSG00000032872" "ENSMUSG00000063694" ...write.csv(results_genes_unique_old1, "results/tables/diff_expr_resultsF_oryg_annot_uniq.csv", row.names = FALSE)Checking uniquness of Probes and Genes How many ENSEMBL with more than 1 Probe
symbol_probe_counts <- results_genes_unique_old1 %>%
group_by(ENSEMBL) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 1symbol_probe_counts## # A tibble: 1 × 2
## ENSEMBL n_probes
## <chr> <int>
## 1 <NA> 186How many SYMBOL with more than 1 Probe
symbol_probe_counts <- results_genes_unique_old1 %>%
group_by(SYMBOL) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 0symbol_probe_counts## # A tibble: 0 × 2
## # ℹ 2 variables: SYMBOL <chr>, n_probes <int>How many Probes mapping to more than 1 ENSEMBL
probe_symbol_counts <- results_genes_unique_old1 %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(ENSEMBL)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) ## [1] 0probe_symbol_counts## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>probe_symbol_counts <- results_genes_unique_old1 %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(SYMBOL)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) #' How many Probes mapping to more than 1 SYMBOL## [1] 0probe_symbol_counts## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>Using Biomart adnotation from Ensembl GRCm39 ver 114. (28.05.2025) Loading Biomart adnotation
annot_new <- read.table("../mart_export_Final.txt", sep = "\t", header = TRUE, stringsAsFactors = FALSE)
annot_new$MGI_symbol <- NULL
str(annot_new)## 'data.frame': 109541 obs. of 3 variables:
## $ ENSEMBL: chr "ENSMUSG00000064336" "ENSMUSG00000064336" "ENSMUSG00000064336" "ENSMUSG00000064337" ...
## $ PROBEID: int 10598020 10598018 10598023 10598020 10598018 10598023 10598025 10598023 10598025 10598027 ...
## $ SYMBOL : chr "mt-Tf" "mt-Tf" "mt-Tf" "mt-Rnr1" ...head(annot_new)## ENSEMBL PROBEID SYMBOL
## 1 ENSMUSG00000064336 10598020 mt-Tf
## 2 ENSMUSG00000064336 10598018 mt-Tf
## 3 ENSMUSG00000064336 10598023 mt-Tf
## 4 ENSMUSG00000064337 10598020 mt-Rnr1
## 5 ENSMUSG00000064337 10598018 mt-Rnr1
## 6 ENSMUSG00000064337 10598023 mt-Rnr1Merging DE results with new annotation
results_annot_new <- merge(resultsF, annot_new, by.x = "row.names", by.y = "PROBEID")
head(results_annot_new)## Row.names logFC CI.L CI.R AveExpr t P.Value
## 1 10338074 -0.06667961 -0.27720381 0.14384459 12.130281 -0.6817806 0.50692211
## 2 10338075 -0.28691723 -0.52697809 -0.04685637 8.840208 -2.5726983 0.02264609
## 3 10338076 0.22366797 -0.07914274 0.52647868 9.355779 1.5899598 0.13501230
## 4 10338077 -0.13996187 -0.41329318 0.13336944 11.509166 -1.1022343 0.28964868
## 5 10338084 0.09433442 -0.27233280 0.46100165 8.002068 0.5537984 0.58878485
## 6 10338084 0.09433442 -0.27233280 0.46100165 8.002068 0.5537984 0.58878485
## adj.P.Val B ENSEMBL SYMBOL
## 1 0.7160388 -6.140468 ENSMUSG00000030967 Zranb1
## 2 0.1808699 -3.586456 ENSMUSG00000032112 Trappc4
## 3 0.3742799 -5.172681 ENSMUSG00000079477 Rab7
## 4 0.5354559 -5.772491 ENSMUSG00000020936 Nmt1
## 5 0.7714536 -6.220642 ENSMUSG00002075586 Gm54825
## 6 0.7714536 -6.220642 ENSMUSG00000071415 Rpl23Adding ProbeId Column instead of rownames
colnames(results_annot_new)[1] <- "ProbeID"
str(results_annot_new)## 'data.frame': 28621 obs. of 11 variables:
## $ ProbeID : chr "10338074" "10338075" "10338076" "10338077" ...
## $ logFC : num -0.0667 -0.2869 0.2237 -0.14 0.0943 ...
## $ CI.L : num -0.2772 -0.527 -0.0791 -0.4133 -0.2723 ...
## $ CI.R : num 0.1438 -0.0469 0.5265 0.1334 0.461 ...
## $ AveExpr : num 12.13 8.84 9.36 11.51 8 ...
## $ t : num -0.682 -2.573 1.59 -1.102 0.554 ...
## $ P.Value : num 0.5069 0.0226 0.135 0.2896 0.5888 ...
## $ adj.P.Val: num 0.716 0.181 0.374 0.535 0.771 ...
## $ B : num -6.14 -3.59 -5.17 -5.77 -6.22 ...
## $ ENSEMBL : chr "ENSMUSG00000030967" "ENSMUSG00000032112" "ENSMUSG00000079477" "ENSMUSG00000020936" ...
## $ SYMBOL : chr "Zranb1" "Trappc4" "Rab7" "Nmt1" ...filtering out rows without SYMBOL or ENSEMBL
results_annot_new <- results_annot_new %>%
filter(
(!is.na(SYMBOL) & SYMBOL != "") |
(!is.na(ENSEMBL) & ENSEMBL != "")
)
str(results_annot_new)## 'data.frame': 28621 obs. of 11 variables:
## $ ProbeID : chr "10338074" "10338075" "10338076" "10338077" ...
## $ logFC : num -0.0667 -0.2869 0.2237 -0.14 0.0943 ...
## $ CI.L : num -0.2772 -0.527 -0.0791 -0.4133 -0.2723 ...
## $ CI.R : num 0.1438 -0.0469 0.5265 0.1334 0.461 ...
## $ AveExpr : num 12.13 8.84 9.36 11.51 8 ...
## $ t : num -0.682 -2.573 1.59 -1.102 0.554 ...
## $ P.Value : num 0.5069 0.0226 0.135 0.2896 0.5888 ...
## $ adj.P.Val: num 0.716 0.181 0.374 0.535 0.771 ...
## $ B : num -6.14 -3.59 -5.17 -5.77 -6.22 ...
## $ ENSEMBL : chr "ENSMUSG00000030967" "ENSMUSG00000032112" "ENSMUSG00000079477" "ENSMUSG00000020936" ...
## $ SYMBOL : chr "Zranb1" "Trappc4" "Rab7" "Nmt1" ...head(results_annot_new)## ProbeID logFC CI.L CI.R AveExpr t P.Value
## 1 10338074 -0.06667961 -0.27720381 0.14384459 12.130281 -0.6817806 0.50692211
## 2 10338075 -0.28691723 -0.52697809 -0.04685637 8.840208 -2.5726983 0.02264609
## 3 10338076 0.22366797 -0.07914274 0.52647868 9.355779 1.5899598 0.13501230
## 4 10338077 -0.13996187 -0.41329318 0.13336944 11.509166 -1.1022343 0.28964868
## 5 10338084 0.09433442 -0.27233280 0.46100165 8.002068 0.5537984 0.58878485
## 6 10338084 0.09433442 -0.27233280 0.46100165 8.002068 0.5537984 0.58878485
## adj.P.Val B ENSEMBL SYMBOL
## 1 0.7160388 -6.140468 ENSMUSG00000030967 Zranb1
## 2 0.1808699 -3.586456 ENSMUSG00000032112 Trappc4
## 3 0.3742799 -5.172681 ENSMUSG00000079477 Rab7
## 4 0.5354559 -5.772491 ENSMUSG00000020936 Nmt1
## 5 0.7714536 -6.220642 ENSMUSG00002075586 Gm54825
## 6 0.7714536 -6.220642 ENSMUSG00000071415 Rpl23write.csv(results_annot_new, "results/tables/diff_expr_resultsF_newannot.csv", row.names = FALSE)Checking uniquness of the Probes and Genes How many ENSEMBL with more than 1 Probe
symbol_probe_counts <- results_annot_new %>%
group_by(ENSEMBL) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 3103How many SYMBOL with more than 1 Probe
symbol_probe_counts <- results_annot_new %>%
group_by(SYMBOL) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 2884How many Probes mapping to more than 1 ENSEMBL
probe_symbol_counts <- results_annot_new %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(ENSEMBL)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) ## [1] 2571How many Probes mapping to more than 1 SYMBOL
probe_symbol_counts <- results_annot_new %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(SYMBOL)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) ## [1] 2500Solving problems with Non unique Genes and Probes List of ProbeIDs with more than one gene based on SYMBOL or ENSEMBL
conflict_ids <- results_annot_new %>%
group_by(ProbeID) %>%
filter(n_distinct(SYMBOL) > 1 | n_distinct(ENSEMBL) > 1) %>%
pull(ProbeID) %>%
unique()
length(conflict_ids)## [1] 2571Removal of ProbeIDs with nonunique Genes If ProbeID with just 1 row - stays If SYMBOLs with the same ENSEMBL have common core, randomly choose one row. Other way remove rows.
filtered_results_new <- results_annot_new %>%
group_by(ProbeID) %>%
group_modify(~ {
subdf <- .x
if (nrow(subdf) == 1) return(subdf)
unique_symbols <- unique(subdf$SYMBOL)
unique_symbols <- unique_symbols[!is.na(unique_symbols) & unique_symbols != ""]
unique_ensembls <- unique(subdf$ENSEMBL)
unique_ensembls <- unique_ensembls[!is.na(unique_ensembls) & unique_ensembls != ""]
roots <- stringr::str_extract(unique_symbols, "^[A-Za-z]{3,}")
roots <- na.omit(roots)
common_root <- length(roots) > 0 && length(unique(roots)) == 1
single_valid_ensembl <- length(unique_ensembls) == 1
if (common_root && single_valid_ensembl) {
return(subdf[sample(nrow(subdf), 1), ])
} else {
return(subdf[0, ])
}
}) %>%
ungroup()
str(filtered_results_new)## tibble [13,588 × 11] (S3: tbl_df/tbl/data.frame)
## $ ProbeID : chr [1:13588] "10338074" "10338075" "10338076" "10338077" ...
## $ logFC : num [1:13588] -0.0667 -0.2869 0.2237 -0.14 -0.3049 ...
## $ CI.L : num [1:13588] -0.2772 -0.527 -0.0791 -0.4133 -0.4948 ...
## $ CI.R : num [1:13588] 0.1438 -0.0469 0.5265 0.1334 -0.115 ...
## $ AveExpr : num [1:13588] 12.13 8.84 9.36 11.51 11.06 ...
## $ t : num [1:13588] -0.682 -2.573 1.59 -1.102 -3.456 ...
## $ P.Value : num [1:13588] 0.50692 0.02265 0.13501 0.28965 0.00406 ...
## $ adj.P.Val: num [1:13588] 0.716 0.1809 0.3743 0.5355 0.0925 ...
## $ B : num [1:13588] -6.14 -3.59 -5.17 -5.77 -1.96 ...
## $ ENSEMBL : chr [1:13588] "ENSMUSG00000030967" "ENSMUSG00000032112" "ENSMUSG00000079477" "ENSMUSG00000020936" ...
## $ SYMBOL : chr [1:13588] "Zranb1" "Trappc4" "Rab7" "Nmt1" ...Make pairs by SYMBOL
symbol_edges <- filtered_results_new %>%
filter(!is.na(SYMBOL) & SYMBOL != "") %>%
group_by(SYMBOL) %>%
filter(n() > 1) %>%
reframe(pairs = combn(ProbeID, 2, simplify = FALSE))
nrow(symbol_edges)## [1] 15112Make pairs by ENSEMBL
ensembl_edges <- filtered_results_new %>%
filter(!is.na(ENSEMBL) & ENSEMBL != "") %>%
group_by(ENSEMBL) %>%
filter(n() > 1) %>%
reframe(pairs = combn(ProbeID, 2, simplify = FALSE))
nrow(ensembl_edges)## [1] 15114Connecting pairs lists
edges <- bind_rows(symbol_edges, ensembl_edges) %>%
pull(pairs)
length(edges)## [1] 30226Making data.frame
edge_df <- do.call(rbind, lapply(edges, function(x) data.frame(from = x[1], to = x[2])))
str(edge_df)## 'data.frame': 30226 obs. of 2 variables:
## $ from: chr "10519179" "10340510" "10340510" "10341744" ...
## $ to : chr "10519181" "10341744" "10437263" "10437263" ...Creating graph
g <- graph_from_data_frame(edge_df, directed = FALSE)
clusters <- components(g)Annotatioing genes with clusters
cluster_map <- data.frame(ProbeID = names(clusters$membership),
gene_cluster = paste0("C", clusters$membership))Joining clusters with z ProbeId, ENsembl, Symbol i DE
filtered_results_new_clustered <- filtered_results_new %>%
left_join(cluster_map, by = "ProbeID") %>%
mutate(gene_cluster = ifelse(is.na(gene_cluster), paste0("single_", ProbeID), gene_cluster))Choose best ProbeiD by FDR or LogFC
results_genes_unique_new <- filtered_results_new_clustered %>%
group_by(gene_cluster) %>%
arrange(adj.P.Val, desc(abs(logFC))) %>%
summarise(best_row = list(first(cur_data())), .groups = "drop") %>%
unnest(best_row) %>%
dplyr::select(-gene_cluster) %>%
as.data.frame()
head(results_genes_unique_new)## ProbeID logFC CI.L CI.R AveExpr t P.Value
## 1 10519179 0.07262673 -0.14246846 0.28772191 9.801597 0.7268075 0.479774811
## 2 10554045 0.50220015 0.28834825 0.71605205 8.177063 5.0549552 0.000197222
## 3 10591622 0.28323591 0.08941603 0.47705579 10.042017 3.1456006 0.007442746
## 4 10364856 0.29456008 0.11274592 0.47637423 11.516333 3.4873841 0.003814862
## 5 10343405 -0.24754960 -0.51034389 0.01524469 9.726731 -2.0276822 0.062834560
## 6 10368068 0.21639148 -0.04646521 0.47924818 8.147441 1.7720449 0.098974580
## adj.P.Val B ENSEMBL SYMBOL
## 1 0.69551053 -6.1085740 ENSMUSG00000096221 1500002C15Rik
## 2 0.02246447 0.9415169 ENSMUSG00000058145 Adamts17
## 3 0.12106678 -2.5420019 ENSMUSG00000032198 Dock6
## 4 0.09103721 -1.9053815 ENSMUSG00000061589 Dot1l
## 5 0.26719623 -4.5135722 ENSMUSG00000026810 Dpm2
## 6 0.32626035 -4.9101970 ENSMUSG00000071392 Ect2lstr(results_genes_unique_new)## 'data.frame': 11920 obs. of 11 variables:
## $ ProbeID : chr "10519179" "10554045" "10591622" "10364856" ...
## $ logFC : num 0.0726 0.5022 0.2832 0.2946 -0.2475 ...
## $ CI.L : num -0.1425 0.2883 0.0894 0.1127 -0.5103 ...
## $ CI.R : num 0.2877 0.7161 0.4771 0.4764 0.0152 ...
## $ AveExpr : num 9.8 8.18 10.04 11.52 9.73 ...
## $ t : num 0.727 5.055 3.146 3.487 -2.028 ...
## $ P.Value : num 0.479775 0.000197 0.007443 0.003815 0.062835 ...
## $ adj.P.Val: num 0.6955 0.0225 0.1211 0.091 0.2672 ...
## $ B : num -6.109 0.942 -2.542 -1.905 -4.514 ...
## $ ENSEMBL : chr "ENSMUSG00000096221" "ENSMUSG00000058145" "ENSMUSG00000032198" "ENSMUSG00000061589" ...
## $ SYMBOL : chr "1500002C15Rik" "Adamts17" "Dock6" "Dot1l" ...write.csv(results_genes_unique_new, "results/tables/diff_expr_resultsF_new_annot_uniq.csv", row.names = FALSE)Checking uniquness of Probes and Genes How many ENSEMBL with more than 1 Probe
symbol_probe_counts <- results_genes_unique_new %>%
group_by(ENSEMBL) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 0symbol_probe_counts## # A tibble: 0 × 2
## # ℹ 2 variables: ENSEMBL <chr>, n_probes <int>How many SYMBOL with more than 1 Probe
symbol_probe_counts <- results_genes_unique_new %>%
group_by(SYMBOL) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 1symbol_probe_counts## # A tibble: 1 × 2
## SYMBOL n_probes
## <chr> <int>
## 1 "" 65How many Probes mapping to more than 1 ENSEMBL
probe_symbol_counts <- results_genes_unique_new %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(ENSEMBL)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) ## [1] 0probe_symbol_counts## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>How many Probes mapping to more than 1 SYMBOL
probe_symbol_counts <- results_genes_unique_new %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(SYMBOL)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) ## [1] 0probe_symbol_counts## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>Merging DE tables with Oryginal and New annotation one set of statistics columns and annotations for both df1 - Oryginal and df2 - New annotations. genes from new Annotation: results_genes_unique_new GENES FROM Oryginal annotation: results_genes_unique_old1 Loading Oryginal and New annotations
df1 <- results_genes_unique_old1
df2 <- results_genes_unique_newExtract statistics and annotations from df1 and df2 per ProbeID
df1_core <- df1 %>% dplyr::select(ProbeID, logFC, CI.L, CI.R, AveExpr, t, P.Value, adj.P.Val, B)
df1_annot <- df1 %>% dplyr::select(ProbeID, SYMBOL, ENSEMBL) %>%
dplyr::rename(SYMBOL.df1 = SYMBOL, ENSEMBL.df1 = ENSEMBL)
df2_core <- df2 %>% dplyr::select(ProbeID, logFC, CI.L, CI.R, AveExpr, t, P.Value, adj.P.Val, B)
df2_annot <- df2 %>% dplyr::select(ProbeID, SYMBOL, ENSEMBL) %>%
dplyr::rename(SYMBOL.df2 = SYMBOL, ENSEMBL.df2 = ENSEMBL)Setting lists common and unique ProbeIds
common_ids <- intersect(df1$ProbeID, df2$ProbeID)
only_df1_ids <- setdiff(df1$ProbeID, df2$ProbeID)
only_df2_ids <- setdiff(df2$ProbeID, df1$ProbeID)Making lists of common rows from df1 and df2 with same statistics and different annotations
common_core <- df1_core %>% filter(ProbeID %in% common_ids)
common_annot_df1 <- df1_annot %>% filter(ProbeID %in% common_ids)
common_annot_df2 <- df2_annot %>% filter(ProbeID %in% common_ids)Making combined table with common Ids and diferential annotation
common_combined <- common_core %>%
left_join(common_annot_df1, by = "ProbeID") %>%
left_join(common_annot_df2, by = "ProbeID") %>%
mutate(status = "common")
str(common_combined)## 'data.frame': 10280 obs. of 14 variables:
## $ ProbeID : chr "10394783" "10531181" "10587627" "10448559" ...
## $ logFC : num 0.4118 0.1685 0.0361 0.2136 -0.1938 ...
## $ CI.L : num -0.0519 -0.0297 -0.1651 -0.0959 -0.4116 ...
## $ CI.R : num 0.875 0.367 0.237 0.523 0.024 ...
## $ AveExpr : num 9.46 8.06 10.22 7.93 8.95 ...
## $ t : num 1.912 1.83 0.386 1.486 -1.915 ...
## $ P.Value : num 0.0774 0.0894 0.7052 0.1604 0.0769 ...
## $ adj.P.Val : num 0.292 0.312 0.848 0.401 0.291 ...
## $ B : num -4.7 -4.82 -6.3 -5.31 -4.69 ...
## $ SYMBOL.df1 : chr "1700030C10Rik" "Adamts3" "Cyb5r4" "D330041H03Rik" ...
## $ ENSEMBL.df1: chr "ENSMUSG00000099759" "ENSMUSG00000043635" "ENSMUSG00000032872" "ENSMUSG00000073437" ...
## $ SYMBOL.df2 : chr "Gm49327" "Adamts3" "Cyb5r4" "D330041H03Rik" ...
## $ ENSEMBL.df2: chr "ENSMUSG00000121309" "ENSMUSG00000043635" "ENSMUSG00000032872" "ENSMUSG00000073437" ...
## $ status : chr "common" "common" "common" "common" ...Extracting df1 specific rows
unique_df1 <- df1_core %>%
filter(ProbeID %in% only_df1_ids) %>%
left_join(df1_annot, by = "ProbeID") %>%
mutate(SYMBOL.df2 = NA, ENSEMBL.df2 = NA, status = "only_in_df1")Extracting df2 specific rows
unique_df2 <- df2_core %>%
filter(ProbeID %in% only_df2_ids) %>%
left_join(df2_annot, by = "ProbeID") %>%
mutate(SYMBOL.df1 = NA, ENSEMBL.df1 = NA, status = "only_in_df2")Combine all rows
combined_all <- bind_rows(common_combined, unique_df1, unique_df2) %>%
arrange(ProbeID)
str(combined_all)## 'data.frame': 12747 obs. of 14 variables:
## $ ProbeID : chr "10338120" "10338286" "10338294" "10338316" ...
## $ logFC : num -0.4206 0.137 -0.0109 0.3112 -0.1588 ...
## $ CI.L : num -0.68527 -0.04955 -0.25806 0.00891 -0.47977 ...
## $ CI.R : num -0.156 0.324 0.236 0.614 0.162 ...
## $ AveExpr : num 9.73 11.91 9.29 8.49 9.18 ...
## $ t : num -3.4215 1.5808 -0.0949 2.216 -1.0649 ...
## $ P.Value : num 0.00434 0.1371 0.92576 0.04446 0.30562 ...
## $ adj.P.Val : num 0.0952 0.3759 0.9672 0.2339 0.5487 ...
## $ B : num -2.03 -5.19 -6.37 -4.2 -5.81 ...
## $ SYMBOL.df1 : chr NA NA NA NA ...
## $ ENSEMBL.df1: chr NA NA NA NA ...
## $ SYMBOL.df2 : chr "Psma1" "Eif5" "" "Dcdc2b" ...
## $ ENSEMBL.df2: chr "ENSMUSG00000030751" "ENSMUSG00000021282" "ENSMUSG00000123626" "ENSMUSG00000078552" ...
## $ status : chr "only_in_df2" "only_in_df2" "only_in_df2" "only_in_df2" ...head(combined_all)## ProbeID logFC CI.L CI.R AveExpr t
## 1 10338120 -0.42064003 -0.685272063 -0.15600800 9.734361 -3.42154126
## 2 10338286 0.13698607 -0.049549813 0.32352196 11.909141 1.58076609
## 3 10338294 -0.01090092 -0.258063142 0.23626130 9.289402 -0.09493682
## 4 10338316 0.31124142 0.008905418 0.61357742 8.489829 2.21595590
## 5 10338366 -0.15879425 -0.479770947 0.16218244 9.181339 -1.06491481
## 6 10338486 -0.27127064 -0.463191264 -0.07935003 10.227305 -3.04252920
## P.Value adj.P.Val B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2
## 1 0.004338430 0.09523126 -2.028254 <NA> <NA> Psma1
## 2 0.137100711 0.37587308 -5.185438 <NA> <NA> Eif5
## 3 0.925761643 0.96716779 -6.374166 <NA> <NA>
## 4 0.044460876 0.23393850 -4.203989 <NA> <NA> Dcdc2b
## 5 0.305616368 0.54867358 -5.811225 <NA> <NA> Gm47260
## 6 0.009104184 0.13010425 -2.732831 <NA> <NA> Psmc5
## ENSEMBL.df2 status
## 1 ENSMUSG00000030751 only_in_df2
## 2 ENSMUSG00000021282 only_in_df2
## 3 ENSMUSG00000123626 only_in_df2
## 4 ENSMUSG00000078552 only_in_df2
## 5 ENSMUSG00000113328 only_in_df2
## 6 ENSMUSG00000020708 only_in_df2common annotation table
common_only <- combined_all %>%
filter(status == "common")
str(common_only)## 'data.frame': 10280 obs. of 14 variables:
## $ ProbeID : chr "10344633" "10344637" "10344658" "10344707" ...
## $ logFC : num -0.0337 -0.0848 -0.0362 -0.2313 -0.0754 ...
## $ CI.L : num -0.221 -0.275 -0.227 -0.416 -0.41 ...
## $ CI.R : num 0.1536 0.1052 0.1549 -0.0465 0.2592 ...
## $ AveExpr : num 11.36 11.12 12.33 9.78 9.89 ...
## $ t : num -0.387 -0.961 -0.408 -2.695 -0.485 ...
## $ P.Value : num 0.7048 0.3536 0.6898 0.0179 0.6352 ...
## $ adj.P.Val : num 0.848 0.595 0.84 0.168 0.804 ...
## $ B : num -6.3 -5.91 -6.29 -3.37 -6.26 ...
## $ SYMBOL.df1 : chr "Tcea1" "Atp6v1h" "Rb1cc1" "Pcmtd1" ...
## $ ENSEMBL.df1: chr "ENSMUSG00000033813" "ENSMUSG00000033793" "ENSMUSG00000025907" "ENSMUSG00000051285" ...
## $ SYMBOL.df2 : chr "Tcea1" "Atp6v1h" "Rb1cc1" "Pcmtd1" ...
## $ ENSEMBL.df2: chr "ENSMUSG00000033813" "ENSMUSG00000033793" "ENSMUSG00000025907" "ENSMUSG00000051285" ...
## $ status : chr "common" "common" "common" "common" ...head(common_only)## ProbeID logFC CI.L CI.R AveExpr t P.Value
## 1 10344633 -0.03365629 -0.2208716 0.1535590 11.362263 -0.3869711 0.70481722
## 2 10344637 -0.08481478 -0.2748344 0.1052049 11.123007 -0.9607860 0.35357609
## 3 10344658 -0.03621075 -0.2273545 0.1549330 12.333149 -0.4077848 0.68983356
## 4 10344707 -0.23134278 -0.4161381 -0.0465474 9.779085 -2.6947498 0.01790379
## 5 10344723 -0.07543749 -0.4100356 0.2591607 9.885885 -0.4853078 0.63524949
## 6 10344725 0.17728497 -0.1146897 0.4692596 8.536757 1.3070145 0.21306273
## adj.P.Val B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2
## 1 0.8480457 -6.301155 Tcea1 ENSMUSG00000033813 Tcea1
## 2 0.5947829 -5.913296 Atp6v1h ENSMUSG00000033793 Atp6v1h
## 3 0.8395928 -6.292624 Rb1cc1 ENSMUSG00000025907 Rb1cc1
## 4 0.1684237 -3.368097 Pcmtd1 ENSMUSG00000051285 Pcmtd1
## 5 0.8040888 -6.257034 Rrs1 ENSMUSG00000061024 Rrs1
## 6 0.4586216 -5.540863 Adhfe1 ENSMUSG00000025911 Adhfe1
## ENSEMBL.df2 status
## 1 ENSMUSG00000033813 common
## 2 ENSMUSG00000033793 common
## 3 ENSMUSG00000025907 common
## 4 ENSMUSG00000051285 common
## 5 ENSMUSG00000061024 common
## 6 ENSMUSG00000025911 commonOrriginal annotation table
df1_only <- combined_all %>%
filter(status == "only_in_df1")
str(df1_only)## 'data.frame': 827 obs. of 14 variables:
## $ ProbeID : chr "10344624" "10344719" "10344741" "10345228" ...
## $ logFC : num -0.118 -0.0595 -0.1345 -0.0667 0.0968 ...
## $ CI.L : num -0.2925 -0.2346 -0.3353 -0.2527 -0.0774 ...
## $ CI.R : num 0.0565 0.1155 0.0663 0.1193 0.271 ...
## $ AveExpr : num 12.08 9.02 11.89 8.94 8.34 ...
## $ t : num -1.455 -0.732 -1.442 -0.772 1.196 ...
## $ P.Value : num 0.169 0.477 0.172 0.454 0.252 ...
## $ adj.P.Val : num 0.411 0.693 0.415 0.675 0.499 ...
## $ B : num -5.35 -6.1 -5.37 -6.07 -5.67 ...
## $ SYMBOL.df1 : chr "Lypla1" "Gm35144" "Hnrnpa3" "1700001G17Rik" ...
## $ ENSEMBL.df1: chr "ENSMUSG00000025903" NA "ENSMUSG00000059005" "ENSMUSG00000103746" ...
## $ SYMBOL.df2 : chr NA NA NA NA ...
## $ ENSEMBL.df2: chr NA NA NA NA ...
## $ status : chr "only_in_df1" "only_in_df1" "only_in_df1" "only_in_df1" ...head(df1_only)## ProbeID logFC CI.L CI.R AveExpr t P.Value
## 1 10344624 -0.11796296 -0.29245601 0.05653009 12.078768 -1.4551948 0.1685031
## 2 10344719 -0.05951958 -0.23455063 0.11551147 9.022949 -0.7319786 0.4767145
## 3 10344741 -0.13447443 -0.33526945 0.06632059 11.890702 -1.4415854 0.1722436
## 4 10345228 -0.06668892 -0.25269667 0.11931882 8.940137 -0.7717493 0.4535790
## 5 10345411 0.09677839 -0.07739997 0.27095674 8.339542 1.1960182 0.2523021
## 6 10346109 0.04937092 -0.13691799 0.23565982 11.825134 0.5704765 0.5777395
## adj.P.Val B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2 ENSEMBL.df2
## 1 0.4106491 -5.354516 Lypla1 ENSMUSG00000025903 <NA> <NA>
## 2 0.6925333 -6.104790 Gm35144 <NA> <NA> <NA>
## 3 0.4145708 -5.372244 Hnrnpa3 ENSMUSG00000059005 <NA> <NA>
## 4 0.6747091 -6.074869 1700001G17Rik ENSMUSG00000103746 <NA> <NA>
## 5 0.4986995 -5.670328 Arhgef4 ENSMUSG00000037509 <NA> <NA>
## 6 0.7644046 -6.211086 Dnah7b ENSMUSG00000041144 <NA> <NA>
## status
## 1 only_in_df1
## 2 only_in_df1
## 3 only_in_df1
## 4 only_in_df1
## 5 only_in_df1
## 6 only_in_df1New annotation table
df2_only <- combined_all %>%
filter(status == "only_in_df2")
str(df2_only)## 'data.frame': 1640 obs. of 14 variables:
## $ ProbeID : chr "10338120" "10338286" "10338294" "10338316" ...
## $ logFC : num -0.4206 0.137 -0.0109 0.3112 -0.1588 ...
## $ CI.L : num -0.68527 -0.04955 -0.25806 0.00891 -0.47977 ...
## $ CI.R : num -0.156 0.324 0.236 0.614 0.162 ...
## $ AveExpr : num 9.73 11.91 9.29 8.49 9.18 ...
## $ t : num -3.4215 1.5808 -0.0949 2.216 -1.0649 ...
## $ P.Value : num 0.00434 0.1371 0.92576 0.04446 0.30562 ...
## $ adj.P.Val : num 0.0952 0.3759 0.9672 0.2339 0.5487 ...
## $ B : num -2.03 -5.19 -6.37 -4.2 -5.81 ...
## $ SYMBOL.df1 : chr NA NA NA NA ...
## $ ENSEMBL.df1: chr NA NA NA NA ...
## $ SYMBOL.df2 : chr "Psma1" "Eif5" "" "Dcdc2b" ...
## $ ENSEMBL.df2: chr "ENSMUSG00000030751" "ENSMUSG00000021282" "ENSMUSG00000123626" "ENSMUSG00000078552" ...
## $ status : chr "only_in_df2" "only_in_df2" "only_in_df2" "only_in_df2" ...head(df2_only)## ProbeID logFC CI.L CI.R AveExpr t
## 1 10338120 -0.42064003 -0.685272063 -0.15600800 9.734361 -3.42154126
## 2 10338286 0.13698607 -0.049549813 0.32352196 11.909141 1.58076609
## 3 10338294 -0.01090092 -0.258063142 0.23626130 9.289402 -0.09493682
## 4 10338316 0.31124142 0.008905418 0.61357742 8.489829 2.21595590
## 5 10338366 -0.15879425 -0.479770947 0.16218244 9.181339 -1.06491481
## 6 10338486 -0.27127064 -0.463191264 -0.07935003 10.227305 -3.04252920
## P.Value adj.P.Val B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2
## 1 0.004338430 0.09523126 -2.028254 <NA> <NA> Psma1
## 2 0.137100711 0.37587308 -5.185438 <NA> <NA> Eif5
## 3 0.925761643 0.96716779 -6.374166 <NA> <NA>
## 4 0.044460876 0.23393850 -4.203989 <NA> <NA> Dcdc2b
## 5 0.305616368 0.54867358 -5.811225 <NA> <NA> Gm47260
## 6 0.009104184 0.13010425 -2.732831 <NA> <NA> Psmc5
## ENSEMBL.df2 status
## 1 ENSMUSG00000030751 only_in_df2
## 2 ENSMUSG00000021282 only_in_df2
## 3 ENSMUSG00000123626 only_in_df2
## 4 ENSMUSG00000078552 only_in_df2
## 5 ENSMUSG00000113328 only_in_df2
## 6 ENSMUSG00000020708 only_in_df2Working on to set the final SYMBOL/ENSEMBL, with rules: If a given row comes only from df1 or df2 (status == “only_in_df1” or “only_in_df2”), we take the data from the corresponding source. If status == “common” (i.e., data is present in both sources): We prefer values from df1, unless the value is NA or ““, in which case we take it from df2. Set final SYMBOL/ENSEMBL Create temporary GENES column being contacanation of SYMBOL_final and ENSEMBL_final
combined_final <- combined_all %>%
mutate(
SYMBOL_final = case_when(
status == "only_in_df1" ~ SYMBOL.df1,
status == "only_in_df2" ~ SYMBOL.df2,
status == "common" & !is.na(SYMBOL.df1) & SYMBOL.df1 != "" ~ SYMBOL.df1,
status == "common" & (is.na(SYMBOL.df1) | SYMBOL.df1 == "") ~ SYMBOL.df2
),
ENSEMBL_final = case_when(
status == "only_in_df1" ~ ENSEMBL.df1,
status == "only_in_df2" ~ ENSEMBL.df2,
status == "common" & !is.na(ENSEMBL.df1) & ENSEMBL.df1 != "" ~ ENSEMBL.df1,
status == "common" & (is.na(ENSEMBL.df1) | ENSEMBL.df1 == "") ~ ENSEMBL.df2
),
GENES = paste0(SYMBOL_final, "_", ENSEMBL_final)
)
head(combined_final)## ProbeID logFC CI.L CI.R AveExpr t
## 1 10338120 -0.42064003 -0.685272063 -0.15600800 9.734361 -3.42154126
## 2 10338286 0.13698607 -0.049549813 0.32352196 11.909141 1.58076609
## 3 10338294 -0.01090092 -0.258063142 0.23626130 9.289402 -0.09493682
## 4 10338316 0.31124142 0.008905418 0.61357742 8.489829 2.21595590
## 5 10338366 -0.15879425 -0.479770947 0.16218244 9.181339 -1.06491481
## 6 10338486 -0.27127064 -0.463191264 -0.07935003 10.227305 -3.04252920
## P.Value adj.P.Val B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2
## 1 0.004338430 0.09523126 -2.028254 <NA> <NA> Psma1
## 2 0.137100711 0.37587308 -5.185438 <NA> <NA> Eif5
## 3 0.925761643 0.96716779 -6.374166 <NA> <NA>
## 4 0.044460876 0.23393850 -4.203989 <NA> <NA> Dcdc2b
## 5 0.305616368 0.54867358 -5.811225 <NA> <NA> Gm47260
## 6 0.009104184 0.13010425 -2.732831 <NA> <NA> Psmc5
## ENSEMBL.df2 status SYMBOL_final ENSEMBL_final
## 1 ENSMUSG00000030751 only_in_df2 Psma1 ENSMUSG00000030751
## 2 ENSMUSG00000021282 only_in_df2 Eif5 ENSMUSG00000021282
## 3 ENSMUSG00000123626 only_in_df2 ENSMUSG00000123626
## 4 ENSMUSG00000078552 only_in_df2 Dcdc2b ENSMUSG00000078552
## 5 ENSMUSG00000113328 only_in_df2 Gm47260 ENSMUSG00000113328
## 6 ENSMUSG00000020708 only_in_df2 Psmc5 ENSMUSG00000020708
## GENES
## 1 Psma1_ENSMUSG00000030751
## 2 Eif5_ENSMUSG00000021282
## 3 _ENSMUSG00000123626
## 4 Dcdc2b_ENSMUSG00000078552
## 5 Gm47260_ENSMUSG00000113328
## 6 Psmc5_ENSMUSG00000020708make additoional temporary columns with info about annotation
combined_final <- combined_final %>%
mutate(
has_symbol = !is.na(SYMBOL_final) & SYMBOL_final != "",
has_ensembl = !is.na(ENSEMBL_final) & ENSEMBL_final != "",
has_both = has_symbol & has_ensembl,
has_any = has_symbol | has_ensembl
)
head(combined_final)## ProbeID logFC CI.L CI.R AveExpr t
## 1 10338120 -0.42064003 -0.685272063 -0.15600800 9.734361 -3.42154126
## 2 10338286 0.13698607 -0.049549813 0.32352196 11.909141 1.58076609
## 3 10338294 -0.01090092 -0.258063142 0.23626130 9.289402 -0.09493682
## 4 10338316 0.31124142 0.008905418 0.61357742 8.489829 2.21595590
## 5 10338366 -0.15879425 -0.479770947 0.16218244 9.181339 -1.06491481
## 6 10338486 -0.27127064 -0.463191264 -0.07935003 10.227305 -3.04252920
## P.Value adj.P.Val B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2
## 1 0.004338430 0.09523126 -2.028254 <NA> <NA> Psma1
## 2 0.137100711 0.37587308 -5.185438 <NA> <NA> Eif5
## 3 0.925761643 0.96716779 -6.374166 <NA> <NA>
## 4 0.044460876 0.23393850 -4.203989 <NA> <NA> Dcdc2b
## 5 0.305616368 0.54867358 -5.811225 <NA> <NA> Gm47260
## 6 0.009104184 0.13010425 -2.732831 <NA> <NA> Psmc5
## ENSEMBL.df2 status SYMBOL_final ENSEMBL_final
## 1 ENSMUSG00000030751 only_in_df2 Psma1 ENSMUSG00000030751
## 2 ENSMUSG00000021282 only_in_df2 Eif5 ENSMUSG00000021282
## 3 ENSMUSG00000123626 only_in_df2 ENSMUSG00000123626
## 4 ENSMUSG00000078552 only_in_df2 Dcdc2b ENSMUSG00000078552
## 5 ENSMUSG00000113328 only_in_df2 Gm47260 ENSMUSG00000113328
## 6 ENSMUSG00000020708 only_in_df2 Psmc5 ENSMUSG00000020708
## GENES has_symbol has_ensembl has_both has_any
## 1 Psma1_ENSMUSG00000030751 TRUE TRUE TRUE TRUE
## 2 Eif5_ENSMUSG00000021282 TRUE TRUE TRUE TRUE
## 3 _ENSMUSG00000123626 FALSE TRUE FALSE TRUE
## 4 Dcdc2b_ENSMUSG00000078552 TRUE TRUE TRUE TRUE
## 5 Gm47260_ENSMUSG00000113328 TRUE TRUE TRUE TRUE
## 6 Psmc5_ENSMUSG00000020708 TRUE TRUE TRUE TRUEKeep only best annotation per ProbeID (df1>common>hasboth>df1>common>df2)
combined_final <- combined_final %>%
group_by(ProbeID) %>%
arrange(
desc(status == "only_in_df1" & has_both),
desc(status == "common" & has_both),
desc(status == "only_in_df1" & has_symbol),
desc(status == "common" & has_symbol),
desc(status == "only_in_df1" & has_any),
desc(status == "common" & has_any),
desc(has_both),
desc(has_symbol),
desc(has_any),
desc(status == "only_in_df1"),
desc(status == "common")
) %>%
slice(1) %>%
ungroup()Remove temporart columns
combined_final <- combined_final %>% dplyr::select(-SYMBOL.df1, -ENSEMBL.df1, -SYMBOL.df2, -ENSEMBL.df2, -has_symbol, -has_ensembl, -has_both, -has_any)
head(combined_final)## # A tibble: 6 × 13
## ProbeID logFC CI.L CI.R AveExpr t P.Value adj.P.Val B
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 10338120 -0.421 -0.685 -0.156 9.73 -3.42 0.00434 0.0952 -2.03
## 2 10338286 0.137 -0.0495 0.324 11.9 1.58 0.137 0.376 -5.19
## 3 10338294 -0.0109 -0.258 0.236 9.29 -0.0949 0.926 0.967 -6.37
## 4 10338316 0.311 0.00891 0.614 8.49 2.22 0.0445 0.234 -4.20
## 5 10338366 -0.159 -0.480 0.162 9.18 -1.06 0.306 0.549 -5.81
## 6 10338486 -0.271 -0.463 -0.0794 10.2 -3.04 0.00910 0.130 -2.73
## # ℹ 4 more variables: status <chr>, SYMBOL_final <chr>, ENSEMBL_final <chr>,
## # GENES <chr>str(combined_final)## tibble [12,747 × 13] (S3: tbl_df/tbl/data.frame)
## $ ProbeID : chr [1:12747] "10338120" "10338286" "10338294" "10338316" ...
## $ logFC : num [1:12747] -0.4206 0.137 -0.0109 0.3112 -0.1588 ...
## $ CI.L : num [1:12747] -0.68527 -0.04955 -0.25806 0.00891 -0.47977 ...
## $ CI.R : num [1:12747] -0.156 0.324 0.236 0.614 0.162 ...
## $ AveExpr : num [1:12747] 9.73 11.91 9.29 8.49 9.18 ...
## $ t : num [1:12747] -3.4215 1.5808 -0.0949 2.216 -1.0649 ...
## $ P.Value : num [1:12747] 0.00434 0.1371 0.92576 0.04446 0.30562 ...
## $ adj.P.Val : num [1:12747] 0.0952 0.3759 0.9672 0.2339 0.5487 ...
## $ B : num [1:12747] -2.03 -5.19 -6.37 -4.2 -5.81 ...
## $ status : chr [1:12747] "only_in_df2" "only_in_df2" "only_in_df2" "only_in_df2" ...
## $ SYMBOL_final : chr [1:12747] "Psma1" "Eif5" "" "Dcdc2b" ...
## $ ENSEMBL_final: chr [1:12747] "ENSMUSG00000030751" "ENSMUSG00000021282" "ENSMUSG00000123626" "ENSMUSG00000078552" ...
## $ GENES : chr [1:12747] "Psma1_ENSMUSG00000030751" "Eif5_ENSMUSG00000021282" "_ENSMUSG00000123626" "Dcdc2b_ENSMUSG00000078552" ...Creating relations ProbeID - SYMBOL, ProbeID - ENSEMBL
symbol_edges <- combined_final %>%
filter(!is.na(SYMBOL_final) & SYMBOL_final != "") %>%
dplyr::select(ProbeID, SYMBOL_final) %>%
rename(gene = SYMBOL_final)
ensembl_edges <- combined_final %>%
filter(!is.na(ENSEMBL_final) & ENSEMBL_final != "") %>%
dplyr::select(ProbeID, ENSEMBL_final) %>%
rename(gene = ENSEMBL_final)
edges <- bind_rows(symbol_edges, ensembl_edges)
g <- graph_from_data_frame(edges, directed = FALSE)
clusters <- components(g)Binding clusters to PRobeID
probe_to_cluster <- data.frame(
ProbeID = names(clusters$membership),
gene_cluster = paste0("G", clusters$membership)
)
combined_clustered <- combined_final %>%
left_join(probe_to_cluster, by = "ProbeID")For each gene group choose one ProbeID df1 > common > df2 > FDR > logFC
final_combined_unique <- combined_clustered %>%
group_by(gene_cluster) %>%
arrange(desc(status == "only_in_df1"), desc(status == "common"),
adj.P.Val, desc(abs(logFC))) %>%
slice(1) %>%
ungroup()Removing gene_cluster column
final_combined_unique <- final_combined_unique %>% dplyr::select(-gene_cluster)Result
final_combined_unique <- as.data.frame(final_combined_unique)
str(final_combined_unique)## 'data.frame': 12585 obs. of 13 variables:
## $ ProbeID : chr "10567072" "10338763" "10344115" "10365136" ...
## $ logFC : num -0.183 -0.493 -0.145 -0.268 -0.102 ...
## $ CI.L : num -0.454 -0.772 -0.607 -0.499 -0.369 ...
## $ CI.R : num 0.0879 -0.2145 0.3163 -0.0368 0.1643 ...
## $ AveExpr : num 10.07 7.84 8.84 9.48 9.41 ...
## $ t : num -1.454 -3.809 -0.678 -2.495 -0.826 ...
## $ P.Value : num 0.16881 0.00204 0.50937 0.02626 0.42316 ...
## $ adj.P.Val : num 0.411 0.0693 0.718 0.1929 0.6498 ...
## $ B : num -5.36 -1.31 -6.14 -3.72 -6.03 ...
## $ status : chr "only_in_df1" "only_in_df2" "only_in_df2" "common" ...
## $ SYMBOL_final : chr "Psma1" "Sap30l" "Gm44187" "Tle5" ...
## $ ENSEMBL_final: chr "ENSMUSG00000030751" "ENSMUSG00000020519" "ENSMUSG00000108268" "ENSMUSG00000054452" ...
## $ GENES : chr "Psma1_ENSMUSG00000030751" "Sap30l_ENSMUSG00000020519" "Gm44187_ENSMUSG00000108268" "Tle5_ENSMUSG00000054452" ...head(final_combined_unique)## ProbeID logFC CI.L CI.R AveExpr t P.Value
## 1 10567072 -0.18296161 -0.4538130 0.08788977 10.071536 -1.4540606 0.16881217
## 2 10338763 -0.49329505 -0.7720810 -0.21450908 7.841442 -3.8088112 0.00204166
## 3 10344115 -0.14538961 -0.6071189 0.31633971 8.839705 -0.6777968 0.50936668
## 4 10365136 -0.26785458 -0.4989202 -0.03678894 9.475127 -2.4952686 0.02626201
## 5 10556246 -0.10233761 -0.3690169 0.16434163 9.413671 -0.8260373 0.42316102
## 6 10556266 -0.09187057 -0.2799978 0.09625666 11.422159 -1.0511830 0.31165275
## adj.P.Val B status SYMBOL_final ENSEMBL_final
## 1 0.41100995 -5.355998 only_in_df1 Psma1 ENSMUSG00000030751
## 2 0.06930072 -1.306324 only_in_df2 Sap30l ENSMUSG00000020519
## 3 0.71803512 -6.143198 only_in_df2 Gm44187 ENSMUSG00000108268
## 4 0.19288391 -3.723343 common Tle5 ENSMUSG00000054452
## 5 0.64978436 -6.031703 common Zfp143 ENSMUSG00000061079
## 6 0.55450067 -5.825196 common Wee1 ENSMUSG00000031016
## GENES
## 1 Psma1_ENSMUSG00000030751
## 2 Sap30l_ENSMUSG00000020519
## 3 Gm44187_ENSMUSG00000108268
## 4 Tle5_ENSMUSG00000054452
## 5 Zfp143_ENSMUSG00000061079
## 6 Wee1_ENSMUSG00000031016Final uniqueness check no of rows without ENSEMBL
sum(is.na(final_combined_unique$ENSEMBL_final) | final_combined_unique$ENSEMBL_final == "") ## [1] 78no of rows without SYMBOL
sum(is.na(final_combined_unique$SYMBOL_final) | final_combined_unique$SYMBOL_final == "") ## [1] 51duplicated ProbeID
any(duplicated(final_combined_unique$ProbeID)) ## [1] FALSEduplicated ENSEMBNL
any(duplicated(final_combined_unique$ENSEMBL_final)) ## [1] TRUEduplicated SYMBOL
any(duplicated(final_combined_unique$SYMBOL_final)) ## [1] TRUEDuplication check how many ENSEMBL with >1 Probe
symbol_probe_counts <- final_combined_unique %>%
group_by(ENSEMBL_final) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 1symbol_probe_counts## # A tibble: 1 × 2
## ENSEMBL_final n_probes
## <chr> <int>
## 1 <NA> 78how many SYMBOL with >1 Probe
symbol_probe_counts <- final_combined_unique %>%
group_by(SYMBOL_final) %>%
summarise(n_probes = n_distinct(ProbeID)) %>%
filter(n_probes > 1)
nrow(symbol_probe_counts) ## [1] 1symbol_probe_counts## # A tibble: 1 × 2
## SYMBOL_final n_probes
## <chr> <int>
## 1 "" 51how many PROBES for more than 1 gene
probe_symbol_counts <- final_combined_unique %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(ENSEMBL_final)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) ## [1] 0probe_symbol_counts## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>how many PROBES for more than 1 gene
probe_symbol_counts <- final_combined_unique %>%
group_by(ProbeID) %>%
summarise(n_symbols = n_distinct(SYMBOL_final)) %>%
filter(n_symbols > 1)
nrow(probe_symbol_counts) ## [1] 0probe_symbol_counts## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>write.csv(final_combined_unique, "results/tables/final_combined_unique.csv", row.names = FALSE)MA Plot
plotMA(fitF, coef = 2, main = "MA plot: KO6 vs KO5", ylim = c(-4, 4))
Volcano Plot FDR < 0.05 & abs(logFC) > 0.5
final_combined_unique$threshold <- final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5
ala <- ggplot(final_combined_unique, aes(x = logFC, y = -log10(P.Value))) +
geom_point(aes(color = threshold)) +
geom_text_repel(data = subset(final_combined_unique, threshold),
aes(label = SYMBOL_final), max.overlaps = 10) +
scale_color_manual(values = c("grey", "red")) +
geom_vline(xintercept = c(-1, -0.5, 0.5, 1), linetype = "dashed", color = "blue") +
theme_minimal() +
labs(title = "Volcano plot: KO6 vs KO5")
ala## Warning: ggrepel: 122 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
final_combined_unique$threshold <- final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5
ala <- ggplot(final_combined_unique, aes(x = logFC, y = -log10(P.Value))) +
geom_point(aes(color = threshold)) +
geom_text_repel(data = subset(final_combined_unique, threshold),
aes(label = ENSEMBL_final), max.overlaps = 10) +
scale_color_manual(values = c("grey", "red")) +
geom_vline(xintercept = c(-1, -0.5, 0.5, 1), linetype = "dashed", color = "blue") +
theme_minimal() +
labs(title = "Volcano plot: KO6 vs KO5")
ala## Warning: Removed 1 row containing missing values or values outside the scale range
## (`geom_text_repel()`).## Warning: ggrepel: 126 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
final_combined_unique$threshold <- final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5
ala <- ggplot(final_combined_unique, aes(x = logFC, y = -log10(P.Value))) +
geom_point(aes(color = threshold)) +
geom_text_repel(data = subset(final_combined_unique, threshold),
aes(label = GENES), max.overlaps = 10) +
scale_color_manual(values = c("grey", "red")) +
geom_vline(xintercept = c(-1, -0.5, 0.5, 1), linetype = "dashed", color = "blue") +
theme_minimal() +
labs(title = "Volcano plot: KO6 vs KO5")
ala## Warning: ggrepel: 130 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
P-value Histogram
hist(final_combined_unique$P.Value, breaks = 50, col = "gray", main = "Histogram p-value")
Heatmap of 100 genes with lowest FDR
top100 <- head(final_combined_unique[order(final_combined_unique$adj.P.Val), ], 100)
top_expr <- plier_gcbg_log_filtered[top100$ProbeID, ]
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(top_expr)
pheatmap(top_expr, scale = "row",
annotation_col = annotation_col,
show_rownames = FALSE,
main = "Heatmapa top 100 genów różnicowych")
Heatmap with 500 genes with lowest FDR
top500 <- head(final_combined_unique[order(final_combined_unique$adj.P.Val), ], 500)
top_expr <- plier_gcbg_log_filtered[top500$ProbeID, ]
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(top_expr)
pheatmap(top_expr, scale = "row",
annotation_col = annotation_col,
show_rownames = FALSE,
main = "Heatmapa top 500 genów różnicowych")
Confidence intervals for log fold change (logFC): For each gene, we calculated the 95% confidence interval (CI) for the estimated log fold change using standard error and the appropriate quantile of the t-distribution. The interval provides a range within which the true logFC is expected to lie with 95% confidence. If the CI includes zero, the change in expression is not considered statistically significant. Narrow intervals indicate precise estimates, while wider intervals reflect greater variability in the data. CI Table (Confidence Interval)
final_combined_unique$Exclude_bio_change <- with(final_combined_unique, CI.L > -0.5 & CI.R < 0.5)
excluded <- final_combined_unique[final_combined_unique$Exclude_bio_change == TRUE, ]
write.csv(excluded, "results/tables/genes_excluded_biological_change_final_combined_unique.csv", row.names = FALSE)CI Plot (Confidence Interval)
plotCI <- head(final_combined_unique[order(final_combined_unique$adj.P.Val), ], 50)
p_plotCI <- ggplot(plotCI, aes(x = reorder(GENES, logFC), y = logFC)) +
geom_point() +
geom_errorbar(aes(ymin = CI.L, ymax = CI.R), width = 0.2) +
geom_hline(yintercept = c(-0.5, -1.0, 0.5, 1.0), linetype = "dashed", color = "red") +
coord_flip() +
theme_minimal() +
labs(title = "LogFC ± CI (top 50)", y = "logFC", x = "Gen")
print(p_plotCI)
Enrichment Analyses List of DE Genes needed by TopGo and gProfiler
de_genes <- final_combined_unique$SYMBOL_final[final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5 & !is.na(final_combined_unique$SYMBOL_final) & final_combined_unique$SYMBOL_final != ""]
str(de_genes)## chr [1:135] "Gdpd3" "Shisa7" "Pop4" "Folh1" "Star" "AI429214" "Slc7a2" ...length(de_genes)## [1] 135de_genesE <- final_combined_unique$ENSEMBL_final[final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5 & !is.na(final_combined_unique$ENSEMBL_final) & final_combined_unique$ENSEMBL_final != ""]
str(de_genesE)## chr [1:136] "ENSMUSG00000030703" "ENSMUSG00000053550" "ENSMUSG00000030423" ...length(de_genesE)## [1] 136de_genesG <- final_combined_unique$GENES[final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5 & !is.na(final_combined_unique$GENES) & final_combined_unique$GENES != ""]
str(de_genesE)## chr [1:136] "ENSMUSG00000030703" "ENSMUSG00000053550" "ENSMUSG00000030423" ...length(de_genesE)## [1] 136FGSEA analysis (GSEA)
categories <- c("BP", "CC", "MF")
gene_ranks <- final_combined_unique$t
names(gene_ranks) <- final_combined_unique$SYMBOL_final[!is.na(final_combined_unique$SYMBOL_final) & final_combined_unique$SYMBOL_final != ""]
length(final_combined_unique$SYMBOL_final[is.na(final_combined_unique$SYMBOL_final) | final_combined_unique$SYMBOL_final == ""])## [1] 51names(gene_ranks)## [1] "Psma1" "Sap30l" "Gm44187" "Tle5"
## [5] "Zfp143" "Wee1" "Swap70" "Gm9132"
## [9] "Mical2" "Parva" "Tead1" "Bmal1"
## [13] "Far1" "Spon1" "Tle2" "Insc"
## [17] "1110004F10Rik" "Gm44777" "Nucb2" "Tmc5"
## [21] "Ccp110" "Vps35l" "Iqck" "Acsm2"
## [25] "Rexo5" "Ankrd24" "Ldaf1" "Anks4b"
## [29] "Abca14" "Abca15" "Abca16" "Gm32916"
## [33] "E130201H02Rik" "Eef2k" "Polr3e" "Mfsd13b"
## [37] "Gm8290" "Mettl9" "Hs3st2" "Ubfd1"
## [41] "Dctn5" "Chp2" "Rbbp6" "Gm20274"
## [45] "Tnrc6a" "Aqp8" "Hs3st4" "Zfp873"
## [49] "4930571K23Rik" "Il4ra" "Katnip" "Sbk1"
## [53] "Rabep2" "Tufm" "Apobr" "Sgf29"
## [57] "Bola2" "Gdpd3" "Gm4924" "Ypel3"
## [61] "Doc2a" "Hirip3" "Kctd13" "Sez6l2"
## [65] "Cdipt" "AI467606" "Fbrs" "Rnf40"
## [69] "Ctf1" "Txnrd1" "Orai3" "Setd1a"
## [73] "Hsd3b7" "Bckdk" "Kat8" "Fus"
## [77] "Itgax" "Itgad" "Armc5" "Slc5a2"
## [81] "1700028I16Rik" "Bag3" "Inpp5f" "Plpp4"
## [85] "Wdr11" "Gm23847" "Plekha1" "Htra1"
## [89] "Fam24a" "Pstk" "Acadsb" "Taf10"
## [93] "Hmx3" "Hmx2" "Bub3" "Gpr26"
## [97] "Gm10584" "Lhpp" "Bccip" "Dock1"
## [101] "Nps" "Foxi2" "Washc4" "Ptpre"
## [105] "Mgmt" "Gm10578" "Glrx3" "Ppp2r2d"
## [109] "Dpysl4" "Pwwp2b" "Adgra1" "Kndc1"
## [113] "Utf1" "Rfk" "Gm47247" "Zfp511"
## [117] "Prap1" "Mtg1" "Or6f2" "Scart2"
## [121] "Or13a19" "Or13a18" "Or13a28" "Urah"
## [125] "Cimap1a" "Gm5425" "Psmd13" "Gm15542"
## [129] "Nlrp6" "Pgghg" "Ifitm1" "B4galnt4"
## [133] "Pkp3" "Lrrc56" "Phrf1" "Drd4"
## [137] "4930463O16Rik" "Tmem80" "Taldo1" "Rangrf"
## [141] "Snora52" "Pnpla2" "Tspan4" "Muc5ac"
## [145] "Brsk2" "Krtap5-3" "Gm45889" "Tcp11l2"
## [149] "Krtap5-4" "Syt8" "Tnni2" "Lsp1"
## [153] "Tnnt3" "Igf2os" "Gm6471" "Cd81"
## [157] "Kcnq1" "Gm15580" "Polr3b" "Dhcr7"
## [161] "Acte1" "Shank2" "Gm10152" "Fgf3"
## [165] "Fgf4" "Fgf15" "LTO1" "Mrgprd"
## [169] "Zc3h3" "Rfx4" "Oscar" "Tfpt"
## [173] "Tmc4" "Mboat7" "Pirb" "Lair1"
## [177] "D030047H15Rik" "Cdc42ep5" "Gm5319" "Rdh13"
## [181] "Ric8b" "Ppp1r12c" "Tnnt1" "Tnni3"
## [185] "Dnaaf3" "Syt5" "Tmem86b" "Ppp6r1"
## [189] "Hspbp1" "Tmem150b" "Cox6b2" "Tmem263"
## [193] "Il11" "Tmem238" "Ube2s" "Shisa7"
## [197] "Isoc2b" "Zfp579" "Zfp784" "Rasl2-9"
## [201] "Zfp787" "Zfp583" "Psma5" "Or6z6"
## [205] "Or10am5" "Peg3" "Zfp954" "Gm45844"
## [209] "Clcn4" "Aurkc" "Zfp551" "Zscan18"
## [213] "Zfp329" "Pwp1" "Zbtb45" "Mzf1"
## [217] "Vmn1r86" "Gm7965" "Zswim9" "Nlrp5-ps"
## [221] "Selenow" "Nop53" "Ehd2" "Bicra"
## [225] "Abhd17a" "Timp3" "C5ar2" "Ccdc9"
## [229] "Sae1" "Npas1" "Fkrp" "Calm3"
## [233] "Ppp5c" "Hif3a" "Gm45150" "Psg23"
## [237] "Gm5174" "Qpctl" "Gipr" "Fosb"
## [241] "Polr1g" "A930016O22Rik" "Mark4" "Bloc1s3"
## [245] "Ppp1r37" "Gemin7" "Clasrp" "Tex18"
## [249] "Apoc4" "Apoc1" "Apoe" "Bcam"
## [253] "Bcl3" "Ceacam19" "Pvr" "Igsf23"
## [257] "Zfp109" "Zfp61" "1700113H08Rik" "Zfp94"
## [261] "Tescl" "Irgc" "Pinlyp" "Tex101"
## [265] "Lypd11" "Cd177" "Rabac1" "Pou2f2"
## [269] "Erf" "Igf1" "Ceacam1" "Cnfn"
## [273] "Cxcl17" "Ceacam2" "Erich4" "Bckdha"
## [277] "Tmem91" "Ccdc97" "Axl" "Cyp2s1"
## [281] "Nup37" "Rpl37a" "Mrpl41" "Egln2"
## [285] "Rab4b" "Mia" "Snrpa" "Itpkc"
## [289] "Ltbp4" "Shkbp1" "Sptbn4" "Washc3"
## [293] "Pld3" "Map3k10" "Zfp974" "Zfp780b"
## [297] "Zfp850" "Psmc4" "Selenov" "Dll3"
## [301] "Timm50" "Supt5" "Gnptab" "Plekhg2"
## [305] "Zfp36" "Med29" "Samd4b" "Ifnl2"
## [309] "Pak4" "Mrps12" "Gm10648" "Actn4"
## [313] "Eif3k" "Sycp3" "Ryr1" "Spred3"
## [317] "Catsperg1" "Kcnk6" "2200002D01Rik" "Spint2"
## [321] "Sipa1l3" "Zfp940" "Zfp566" "Tbcb"
## [325] "Gm47081" "Ovol3" "Wdr62" "Sdhaf1"
## [329] "Lrfn3" "Gm25259" "Hcst" "Aplp1"
## [333] "Kirrel2" "Proser3" "Lin37" "Arfgef1"
## [337] "Cdk17" "Kmt2b" "Zbtb32" "Cox6b1"
## [341] "Etv2" "Haus5" "Pmis2" "Tmem147"
## [345] "Ffar3" "Cd22" "Mag" "Lta4h"
## [349] "Hamp2" "Usf2" "Lsr" "Fxyd5"
## [353] "Fxyd1" "Hpn" "Scn1b" "Gramd1a"
## [357] "Scgb2b23-ps" "Scgb2b26" "Ccdc38" "Gm12760"
## [361] "Wtip" "Uba2" "Pdcd2l" "Lsm14a"
## [365] "Chst8" "Cebpg" "Lrp3" "Wdr88"
## [369] "Gpatch1" "Gm3571" "Faap24" "Tdrd12"
## [373] "Nudt19" "Rgs9bp" "Pdcd5" "Dpy19l3"
## [377] "Zfp507" "Gm22302" "Uri1" "Pop4"
## [381] "Nr2c1" "Gm5114" "AI987944" "Gm20449"
## [385] "Gm7224" "4933421I07Rik" "Gm54949" "Zfp976"
## [389] "Zfp975" "Rpl18a-ps4" "Zfp715" "Tmcc3"
## [393] "Iglon5" "Siglecl2" "Siglecl1" "1700028J19Rik"
## [397] "Acp4" "Gm18307" "1700008O03Rik" "Emc10"
## [401] "Zfp473" "Atf5" "Cep83" "Tbc1d17"
## [405] "Ptov1" "Med25" "D7Bwg0826e" "Cpt1c"
## [409] "Prmt1" "Bcl2l12" "Scaf1" "Prr12"
## [413] "Fcgrt" "Eea1" "Rps11" "Aldh16a1"
## [417] "Kash5" "Cd37" "Trpm4" "Lin7b"
## [421] "Snrnp70" "Dhdh" "Nucb1" "Fgf21"
## [425] "Dcn" "Fut2" "Sec1" "Sphk2"
## [429] "Gm5897" "Cyth2" "Grin2d" "Emp3"
## [433] "Kcnj11" "Abcc8" "Sergef" "Epyc"
## [437] "Saal1" "Hps5" "Uevld" "Gm45737"
## [441] "Ptpn5" "Mrgpra3" "Mrgprb3" "Gm45086"
## [445] "E2f8" "Dbx1" "Acot11" "Ccer1"
## [449] "Fancf" "Svip" "Gm9357" "Gm6290"
## [453] "Nipa2" "Gabra5" "Gm6226" "Snrpn"
## [457] "A230006K03Rik" "Ube2nl" "B530045E10Rik" "Peg12"
## [461] "Chrna7" "Klf13" "Fan1" "Mphosph10"
## [465] "Entrep2" "Nsmce3" "Aldh1a3" "Asb7"
## [469] "Synm" "Cep290" "Gm7627" "Nr2f2"
## [473] "Gm7693" "Gm5335" "Chd2" "A830073O21Rik"
## [477] "Gm10619" "St8sia2" "Mrpl46" "Det1"
## [481] "Mgat4c" "Mfge8" "Polg" "Rhcg"
## [485] "Kif7" "Plin1" "Mesp1" "Ap3s2"
## [489] "Idh2" "Cib1" "Rccd1" "Rassf9"
## [493] "Unc45a" "Fes" "Furin" "Crtc3"
## [497] "Wdr73" "Nmb" "Sec11a" "Rps17"
## [501] "Homer2" "Hdgfl3" "Gm25587" "Bnc1"
## [505] "Saxo2" "Il16" "Cfap161" "Arnt2"
## [509] "Fah" "Zfand6" "Folh1" "Tmem135"
## [513] "Ccdc81" "Ccdc59" "Hikeshi" "Eed"
## [517] "Btf3-ps5" "Ccdc83" "Tmem126a" "Tmem126b"
## [521] "Ankrd42" "4632427E13Rik" "Gm5037" "Gm22226"
## [525] "Ppfia2" "Thrsp" "Aamdc" "Rsf1os2"
## [529] "Capn5" "Omp" "Acer3" "Tsku"
## [533] "A630091E08Rik" "Emsy" "Uvrag" "Pawr"
## [537] "Serpinh1" "Rps3" "Snord15b" "Tpbgl"
## [541] "F730035P03Rik" "Spcs2" "Rnf169" "Pold3"
## [545] "Gm10603" "P2ry6" "Gm23105" "Inppl1"
## [549] "Folr1" "Il18bp" "Rnf121" "Art5"
## [553] "Rhog" "Or55b3" "Or55b10" "Trim21"
## [557] "Trim68" "Vps26c" "E2f7" "Or52r1"
## [561] "Or51s1" "Or51h7" "Or51g2" "Usp17ld"
## [565] "Or52s19" "Or52a5" "Dnajc19-ps" "Or51a42"
## [569] "Or51a43" "Csrp2" "Ubqln5" "Trim30a"
## [573] "Or52n4" "Or52x1" "Or52b2" "Gm4972"
## [577] "Cavin3" "Apbb1" "Trim3" "Arfip2"
## [581] "Rpl6" "Gm22504" "Rrp8" "Tpp1"
## [585] "Mrpl17" "Or2ag15" "Or2ag18" "5330417H12Rik"
## [589] "Cyb5r2" "Ric3" "Stk33" "Osbpl8"
## [593] "Trim66" "BC051019" "Ascl3" "Nrip3"
## [597] "Dennd5a" "Tmem41b" "Rnf141" "Lyve1"
## [601] "Irag1" "Dkk3" "Bbs10" "Rras2"
## [605] "Cyp2r1" "Plekha7" "Pik3c2a" "Gm4366"
## [609] "Arl6ip1" "Smg1" "Itpripl2" "Tmc7"
## [613] "Knop1" "Nap1l1" "Gprc5b" "Gpr139"
## [617] "Umod" "Pdilt" "Thumpd1" "Eri2"
## [621] "Dcun1d3" "Dnah3" "Crym" "Pdzd9"
## [625] "Gm5176" "Cdr2" "Gm9905" "Usp31"
## [629] "Cog7" "Palb2" "Ern2" "Arhgap17"
## [633] "Zkscan2" "4933440M02Rik" "Nsmce1" "Phlda1"
## [637] "Gtf3c1" "Gsg1l" "Lat" "Spns1"
## [641] "Sh2b1" "Il27" "Nupr1" "Sult1a1"
## [645] "Coro1a" "Ppp4c" "Krr1" "Tmem219"
## [649] "Asphd1" "Pagr1a" "Maz" "Kif22"
## [653] "Qprt" "Spn" "Cd2bp2" "Gm4532"
## [657] "Dctpp1" "Glipr1l1" "Zfp768" "Zfp747"
## [661] "Zfp764l1" "Zfp764" "Zfp689" "1700008J07Rik"
## [665] "Zfp629" "1700120K04Rik" "Bcl7c" "Ctf2"
## [669] "Lypla1" "Glipr1l2" "Gm53374" "Stx1b"
## [673] "Zfp668" "Prss53" "Vkorc1" "Prss36"
## [677] "Pycard" "Yipf5" "Cox6a2" "Rusf1"
## [681] "Caps2" "Gm4768" "Nsmce4a" "Cuzd1"
## [685] "Fam24b" "2310057M21Rik" "Gm16477" "Oat"
## [689] "Eef1akmt2" "Ctbp2" "Tex36" "Kcnc2"
## [693] "Dhx32" "D7Ertd443e" "Insyn2a" "Mki67"
## [697] "9430038I01Rik" "Tcerg1l" "Mapk1ip1" "Nkx6-2"
## [701] "Gm4974" "Spef1l" "Gm26596" "Msx3"
## [705] "Caly" "Echs1" "Or6b13" "Syce1"
## [709] "Zfp941" "Ifitm3" "Ifitm6" "Rnh1"
## [713] "Hras" "Gm15723" "Lmntd2" "Mir210"
## [717] "Sct" "Cend1" "Slc25a22" "Pidd1"
## [721] "Gm10575" "Chid1" "Gm16982" "Muc6"
## [725] "Zfc3h1" "Mob2" "Dusp8" "Krtap5-2"
## [729] "Krtap5-24" "Krtap5-1" "Gm5054" "Ctsd"
## [733] "Igf2" "Mir483" "Ins2" "Tspan8"
## [737] "Gm7290" "Ascl2" "Phlda2" "Nap1l4"
## [741] "Gm23297" "Tnfrsf23" "Mrgprg" "Nadsyn1"
## [745] "Cttn" "Ppfia1" "Ptprb" "Fadd"
## [749] "Ano1" "Smim38" "Tpcn2" "Myadm"
## [753] "Cacng7" "Arhgef18" "Saxo5" "Zfp358"
## [757] "Camsap3" "Kcnmb4os2" "Retn" "Trappc5"
## [761] "Evi5l" "Lrrc8e" "Ccl25" "Zfp958"
## [765] "Gm45224" "Gpi1" "Abhd13" "Col4a2"
## [769] "5330438D12Rik" "Naxd" "Ing1" "Arhgef7"
## [773] "Tex29" "Sox1ot" "Sox1" "Spaca7"
## [777] "4931415C17Rik" "Atp11a" "Mcf2l" "Tcea1"
## [781] "Mdm1" "F7" "Cul4a" "Tmco3"
## [785] "Grk1" "Tmem255b" "Cdc16" "Upf3a"
## [789] "Champ1" "Fbxo25" "Dlgap2" "Grip1"
## [793] "Cln8" "Arhgef10" "Kbtbd11" "Mcph1"
## [797] "Agpat5" "Defb46" "Gm16425" "AY761185"
## [801] "Defa26" "Defb35" "Tmbim4" "Ccdc70"
## [805] "Vps36" "Thsd1" "Tpte" "Mrps31"
## [809] "Slc20a2" "Plat" "Ank1" "Nkx6-3"
## [813] "Tm2d2" "4921513I03Rik" "D830025C05Rik" "Lsm1"
## [817] "Star" "Rnf170" "Erlin2" "Plpbp"
## [821] "Tex24" "Dusp26" "Tti2" "Purg"
## [825] "Gns" "Hmgb1-rs17" "Tex15" "Gtf2e2"
## [829] "Mboat4" "Saraf" "Dusp4" "Ppp1r3b"
## [833] "Rps12" "Trmt9b" "AI429214" "D930020B18Rik"
## [837] "Tusc3" "Micu3" "Zdhhc2" "Vps37a"
## [841] "Adam24" "Adam25" "Adam20" "Adam39"
## [845] "Slc7a2" "Gm6180" "Kics2" "Triml2"
## [849] "Gm2221" "Fat1" "Mtnr1a" "Sorbs2"
## [853] "Pdlim3" "Ccdc110" "Cfap97" "Cenpu"
## [857] "Irf2" "Gm9081" "Rwdd4a" "AA386476"
## [861] "E030037K01Rik" "4930555F03Rik" "Aga" "Asb5"
## [865] "Spata4" "Gm47612" "Hpgd" "Fbxo8"
## [869] "Avpr1a" "Hmgb2" "Mfap3l" "Hpf1"
## [873] "B230317F23Rik" "Sh3rf1" "Cbr4" "Ddx60"
## [877] "Tmem192" "Marchf1" "Gm26123" "Gm9102"
## [881] "Naf1" "Sh2d4a" "Atp6v1b2" "Zfp930"
## [885] "Zfp781a" "Atp13a1" "Lpar2" "Pbx4"
## [889] "Tssk6" "Sugp1" "Atp6v1h" "Mettl1"
## [893] "Tm6sf2" "Mef2b" "Tmem161a" "Sugp2"
## [897] "Homer3" "Cope" "Comp" "Fkbp8"
## [901] "Ell" "Isyna1" "Cdk4" "Lsm4"
## [905] "Jund" "Iqcn" "Pde4c" "Il12rb1"
## [909] "A230052G05Rik" "Myo9b" "Use1" "Ocel1"
## [913] "Babam1" "B4galnt1" "Ankle1" "Dda1"
## [917] "Gtpbp3" "Mvb12a" "Slc27a1" "Pgls"
## [921] "Niban3" "Colgalt1" "Jak3" "Gm45756"
## [925] "Dctn2" "Zfp882" "Zfp617" "Zfp961"
## [929] "Tpm4" "Hsh2d" "Fam32a" "Ap1m1"
## [933] "Klf2" "1700030K09Rik" "Atp5mk" "Ddit3"
## [937] "Sin3b" "F2rl3" "Hmgxb4" "Tom1"
## [941] "Hmox1" "Mcm5" "Rasd2" "Iqcm"
## [945] "0610038B21Rik" "Slc10a7" "Stac3" "Otud4"
## [949] "Anapc10" "Gm31223" "Inpp4b" "Mgat4d"
## [953] "Clgn" "Ndufb7" "Dnajb1" "Gipc1"
## [957] "Gm54868" "Ndufa4l2" "Adgrl1" "Asf1b"
## [961] "Prkaca" "1700067K01Rik" "Brme1" "Mir23a"
## [965] "Mir24-2" "Cacna1a" "Gadd45gip1" "Farsa"
## [969] "Stat6" "Syce2" "Klf1" "Dnase2a"
## [973] "Rtbdn" "Prdx2" "Hook2" "Trir"
## [977] "Fbxw9" "Wdr83os" "Man2b1" "Nemp1"
## [981] "Orc6" "Gpt2" "Phkb" "Lonp2"
## [985] "Gm10638" "Rps13" "4933402J07Rik" "9430002A10Rik"
## [989] "Tent4b" "Nkd1" "Myo1a" "Rps6"
## [993] "Chd9" "Fto" "Irx6" "Mmp2"
## [997] "Capns2" "Ces5a" "Gnao1" "Ogfod1"
## [1001] "Mt4" "Rb1cc1" "Zbtb39" "Mt3"
## [1005] "Nup93" "Slc12a3" "Nlrc5" "Ccl22"
## [1009] "Cx3cl1" "Ccl17" "Coq9" "Drc7"
## [1013] "Katnb1" "Prim1" "Spmip8" "Ccdc113"
## [1017] "Gm5912" "Gins3" "A330008L17Rik" "Impdh2"
## [1021] "Gm5742" "Cdh5" "Bean1" "Cmtm3"
## [1025] "Ptges3" "K230015D01Rik" "Car7" "Ces2a"
## [1029] "Gm45725" "Ces3b" "Cbfb" "Phaf1"
## [1033] "Fbxl8" "Hsf4" "E2f4" "Gls2"
## [1037] "Tmem208" "Slc9a5" "Hsd11b2" "Ripor1"
## [1041] "Pard6a" "4933405L10Rik" "Thap11" "Nutf2"
## [1045] "Edc4" "Nrn1l" "Mip" "Pskh1"
## [1049] "Dus2" "Nfatc3" "Prmt7" "Gm10629"
## [1053] "Cdh3" "Tango6" "Utp4" "Sntb2"
## [1057] "Vps4a" "Timeless" "Nip7" "Cyb5b"
## [1061] "Nfat5" "Zfhx3" "Pmfbp1" "Txnl4b"
## [1065] "Pkd1l3" "Zfp821" "Ap1g1" "Zfp612"
## [1069] "Stat2" "Cmtr2" "Hydin" "Vac14"
## [1073] "Mtss2" "Cog4" "Aars1" "Pdpr"
## [1077] "Gm55089" "Znrf1" "Zfp1" "Pan2"
## [1081] "Terf2ip" "Syce1l" "Wwox" "Dynlrb2"
## [1085] "Cenpn" "Atmin" "Cmip" "Plcg2"
## [1089] "Cdh13" "Hsbp1" "Cnpy2" "Necab2"
## [1093] "Dnaaf1" "Adad2" "Wfdc1" "Klhl36"
## [1097] "Crispld2" "Cox4i1" "Irf8" "Foxf1"
## [1101] "Foxc2" "Cs" "Jph3" "BC048644"
## [1105] "Zfp469" "Zfpm1" "Zc3h18" "Il17c"
## [1109] "9330133O14Rik" "Trappc2l" "Gm10612" "Gm16378"
## [1113] "Lamtor5" "Pcmtd1" "Ankrd52" "Cdh15"
## [1117] "Dpep1" "Cdk10" "Zfp276" "Tcf25"
## [1121] "Mc1r" "Tubb3" "Afg3l1" "Gas8"
## [1125] "Rhou" "Rnf41" "Rab4a" "Gm9901"
## [1129] "Gm3889" "Cog2" "Arv1" "Gm9172"
## [1133] "Trim67" "Tsnax" "Disc1" "Map3k21"
## [1137] "Smarcc2" "Kcnk1" "Coa6" "Nrp1"
## [1141] "Gm9204" "Itgb1" "Ccdc7b" "Insr"
## [1145] "Pex11g" "Xab2" "Clec4g" "Pmel"
## [1149] "Cd209a" "Rprl3" "Gm7381" "Cd209d"
## [1153] "Ctxn1" "Timm44" "Elavl1" "Shcbp1"
## [1157] "Gm9457" "Arglu1" "Pym1" "Nalf1"
## [1161] "Lig4" "Gm32429" "Rps16-ps3" "Irs2"
## [1165] "Col4a1" "Cars2" "Ankrd10" "Spaca7b"
## [1169] "Gm45420" "Dnajc14" "Gm15348" "Pcid2"
## [1173] "Grtp1" "Dcun1d2" "Gas6" "1700029H14Rik"
## [1177] "Rasa3" "Semp2l2a" "Tdrp" "Erich1"
## [1181] "Sarnp" "BB014433" "Gm15357" "Defb33"
## [1185] "Defa39" "Defb15" "Atp7b" "Ckap2"
## [1189] "Vdac3" "Polb" "Ap3m2" "Cd63"
## [1193] "Mir3107" "Gins4" "Adam18" "Adam9"
## [1197] "Htra4" "Tacc1" "Ash2l" "Hgsnat"
## [1201] "Pomk" "Fnta" "Or10p21" "Hook3"
## [1205] "Proscos" "Brf2" "Got1l1" "Gm8096"
## [1209] "Unc5d" "Mak16" "Gm8168" "Gm5117"
## [1213] "Nrg1" "Or6c1b" "Gtpbp10" "1700104B16Rik"
## [1217] "Rbpms" "Dctn6" "Gm8254" "Rpl31-ps23"
## [1221] "Eri1" "Gm5787" "Dlc1" "Gm10683"
## [1225] "Gm35144" "Or6c3" "Mir383" "Msr1"
## [1229] "Gm2033" "Cnot7" "Gm8423" "Mtus1"
## [1233] "Asah1" "Frg1" "Zfp353-ps" "Triml1"
## [1237] "Ctdsp2" "Zfp42" "Adam26b" "Adam26a"
## [1241] "Adam34l" "Gm5347" "Gm9908" "Cfap96"
## [1245] "Ankrd37" "Slc25a4" "Primpol" "Gm3213"
## [1249] "Stox2" "Trappc11" "Rps16" "Cdkn2aip"
## [1253] "Tenm3" "Gm6463" "Neil3" "Adam29"
## [1257] "Cep44" "Sap30" "Gm10097" "Gm6012"
## [1261] "Galnt7" "Clcn3" "Palld" "Msmo1"
## [1265] "Klhl2" "Tma16" "Gm7639" "Psd3"
## [1269] "Lzts1" "Esr1" "Gm7684" "Gm10033"
## [1273] "Zfp868" "Zfp869" "Cilp2" "Yjefn3"
## [1277] "Ndufa13" "Gatad2a" "Gm7730" "Armc6"
## [1281] "Akap12" "Ddx49" "Upf1" "Klhl26"
## [1285] "Rex1bd" "Kxd1" "Mpv17l2" "Ifi30"
## [1289] "Pik3r2" "Arrdc2" "Ccdc124" "Gm25515"
## [1293] "Slc5a5" "Rpl18a" "Nr2f6" "Ushbp1"
## [1297] "Abhd8" "Plvap" "Bst2" "Tmem221"
## [1301] "Nxnl1" "Unc13a" "Plekhg1" "B3gnt3"
## [1305] "Gm18860" "Cyp4f18" "Eps15l1" "Calr3"
## [1309] "Cherp" "Large1" "Crry-ps" "Gm22509"
## [1313] "Tmem184c" "Iyd" "Pou4f2" "1700011L22Rik"
## [1317] "Tpd52" "Zc3h15" "4930505O20Rik" "Smarca5"
## [1321] "Gab1" "Usp38" "Gm4899" "Zfp330"
## [1325] "Ppp1r14c" "Gm10645" "Elmod2" "Scoc"
## [1329] "Tecr" "Pkn1" "Adgre5" "Gm10644"
## [1333] "Misp3" "Il27ra" "Rln3" "Rrs1"
## [1337] "Ginm1" "C330011M18Rik" "Dcaf15" "Cc2d1a"
## [1341] "Mir181d" "Mir181c" "Zswim4" "D8Ertd738e"
## [1345] "Yju2b" "Dand5" "Gcdh" "Ust"
## [1349] "Rnaseh2a" "Junb" "Get3" "Wdr83"
## [1353] "Vps35" "4921524J17Rik" "Neto2" "Gm16167"
## [1357] "Siah1a" "Sall1" "Sash1" "Gm6625"
## [1361] "Gm6658" "Aktip" "Rpgrip1l" "Irx3"
## [1365] "Crnde" "Ces1a" "Ces1d" "Nudt21"
## [1369] "Bbs2" "Stxbp5" "Pllp" "Ciapin1"
## [1373] "Kifc3" "Cngb1" "Cfap20" "Prss54"
## [1377] "Slc38a7" "Gm7191" "Cdh11" "Gm10631"
## [1381] "Adgb" "Tk2" "Cmtm4" "Nae1"
## [1385] "Tradd" "Matcap1" "Mir328" "Tppp3"
## [1389] "Zdhhc1" "Enkd1" "Ranbp10" "Grm1"
## [1393] "Ctrl" "Cenpt" "Lcat" "Ddx28"
## [1397] "Esrp2" "Cog8" "Tmed6" "Nob1"
## [1401] "Psmd7" "Gm56822" "Utrn" "Gm1943"
## [1405] "Dhx38" "Ist1" "Atxn1l" "Gm38523"
## [1409] "Glg1" "Mlkl" "Fa2h" "Bcar1"
## [1413] "Cfdp1" "Stx11" "Tmem170" "Chst5"
## [1417] "Adat1" "Kars1" "Maf" "Cdyl2"
## [1421] "Cmc2" "1700030J22Rik" "Gcsh" "Sdr42e1"
## [1425] "Zc2hc1b" "Mphosph6" "Gm45722" "Mbtps1"
## [1429] "Hsdl1" "Cotl1" "Zdhhc7" "Emc8"
## [1433] "Fbxo31" "Zcchc14" "Klhdc4" "Ltv1"
## [1437] "Slc7a5" "Trhr2" "Mvd" "Rnf166"
## [1441] "Piezo1" "Aprt" "Galns" "Cbfa2t3"
## [1445] "Ankrd11" "Chmp1a" "Adhfe1" "Phactr2"
## [1449] "Spata2l" "Fanca" "Dbndd1" "n-R5s136"
## [1453] "Acta1" "Abcb10" "Taf5l" "Pgbd5"
## [1457] "Agt" "2310022B05Rik" "Aig1" "Ttc13"
## [1461] "Fam89a" "Exoc8" "Egln1" "Sipa1l2"
## [1465] "Irf2bp2" "Gm26397" "Rbm34" "Ccdc7a"
## [1469] "A530040E14Rik" "Gje1" "Alkbh8" "Gm24918"
## [1473] "Cwf19l2" "Gucy1a2" "Gm5363" "Kbtbd3"
## [1477] "Msantd4" "Tfdp1" "Pdgfd" "Mmp12"
## [1481] "Heca" "Mmp10" "Gm19324" "1700128F08Rik"
## [1485] "Gm29785" "Cwc15" "Vstm5" "Taf1d"
## [1489] "Smco4" "Gm5119" "Slc36a4" "Abracl"
## [1493] "Gm4977" "Gm7680" "Chordc1" "Ubtfl1"
## [1497] "Or7g30" "Zfp317" "Gm7769" "Zfp846"
## [1501] "Ubl5" "Pin1" "Ect2l" "Rdh8"
## [1505] "Shfl" "Ppan" "Mrpl4" "Icam1"
## [1509] "Icam5" "1700084C06Rik" "Pde4a" "Atg4d"
## [1513] "Qtrt1" "Hebp2" "Dnm2" "AB124611"
## [1517] "Carm1" "Ldlr" "Ccdc159" "Plppr2"
## [1521] "Swsap1" "Prkcsh" "Gm6581" "Pigyl"
## [1525] "Arfgef3" "Zfp872" "Zfp809" "Gm10701"
## [1529] "Cypt4" "Septin7" "Eepd1" "B3gat1"
## [1533] "Thyn1" "Igsf9b" "Spata19" "Gm4922"
## [1537] "Zbtb44" "Tpi-rs4" "Arhgap32" "Kirrel3"
## [1541] "4930581F22Rik" "Srpra" "Rpusd4" "Cdon"
## [1545] "Pus3" "Pate11" "Tnfaip3" "Acrv1"
## [1549] "Fez1" "Tmem218" "Hepacam" "Msantd2"
## [1553] "Siae" "Tpt1" "Or8b8" "Or8c18"
## [1557] "Or8c20" "Hnrnpa3" "Pex7" "Or8b56"
## [1561] "Gm8543" "Or10s1" "Tmem225" "Zfp202"
## [1565] "Clmp" "Hspa8" "Snord14e" "Gm48565"
## [1569] "Bsx" "4933406P04Rik" "Mir100hg" "Gm10690"
## [1573] "Nectin1" "Usp2" "Ccdc153" "Gm10686"
## [1577] "Dpagt1" "H2ax" "Hyou1" "Slc37a4"
## [1581] "Semp2l2b" "Ift46" "Gm39326" "Mpzl2"
## [1585] "Fxyd6" "Fxyd2" "Dscaml1" "Bace1"
## [1589] "Pcsk7" "A830035O19Rik" "Apoa1" "Ube2q2"
## [1593] "Apoa4" "Apoa5" "Zpr1" "Bud13"
## [1597] "Cadm1" "Gm5617" "Usp28" "Zw10"
## [1601] "Tmprss5" "Drd2" "Eya4" "Gm11149"
## [1605] "Pih1d2" "Cryab" "Alg9" "Btg4"
## [1609] "Pou2af1" "Gm32819" "Gm8959" "Arhgap20"
## [1613] "Rdx" "Enpp1" "Btf3-ps15" "Exph5"
## [1617] "4930550C14Rik" "Slc35f2" "Sh2d7" "Ireb2"
## [1621] "Chrna5" "Fbxo22" "Rcn2" "Pstpip1"
## [1625] "Akap7" "Hmg20a" "Cspg4" "Imp3"
## [1629] "Snupn" "Man2c1" "Gm5121" "Fam219b"
## [1633] "Scamp2" "Edc3" "Sema7a" "Gm8681"
## [1637] "Cyp11a1" "1600029O15Rik" "Stoml1" "Gm10657"
## [1641] "Hcn4" "Adpgk" "Celf6" "Parp6"
## [1645] "Myo9a" "Larp6" "L3mbtl3" "1700036A12Rik"
## [1649] "Uaca" "Anp32a" "Itga11" "Calml4"
## [1653] "Gm24526" "Aagab" "Snord16a" "Snapc5"
## [1657] "Tipin" "Gm5649" "Megf11" "Dennd4a"
## [1661] "Ints14" "Igdcc3" "Cilp" "Clpx"
## [1665] "Pdcd7" "Rasl12" "Spg21" "Rbpms2"
## [1669] "Vxn" "Lama2" "Oaz2" "Ppib"
## [1673] "Ciao2a" "Herc1" "Rps27l" "C2cd4b"
## [1677] "Vps13c" "Rora" "Ice2" "Anxa2"
## [1681] "Gm54670" "Gtf2a2" "Myo1e" "Sltm"
## [1685] "Gm10642" "Adam10" "Aldh1a2" "Zfp280d"
## [1689] "Mns1" "Rfx7" "Nedd4" "4930519F09Rik"
## [1693] "Pygo1" "Dnaaf4" "Ccpg1" "Rab27a"
## [1697] "Gm16551" "Onecut1" "Atosa" "Arpp19"
## [1701] "Gnb5" "Leo1" "Rnf146" "Gclc"
## [1705] "Elovl5" "Cilk1" "Gsta4" "Ddx43"
## [1709] "Mto1" "Myo6" "Irak1bp1" "Sh3bgrl2"
## [1713] "Bckdhb" "Cenpw" "Gm26126" "Gm25125"
## [1717] "Dop1a" "Rwdd2a" "Prss35" "Ripply2"
## [1721] "Cyb5r4" "D030062O11Rik" "Nt5e" "Zfp949"
## [1725] "Hint3" "Gm24463" "Rasgrf1" "Ctsh"
## [1729] "Adamts7" "Gm22866" "Plscr1l1" "Plod2"
## [1733] "Paqr9" "Pcolce2" "Gk5" "Supt4a"
## [1737] "Tfdp2" "Rpl7a-ps10" "Nmnat3" "Gm28530"
## [1741] "Rbp1" "Copb2" "Prr23a4" "Foxl2"
## [1745] "Faim" "Dbr1" "Zup1" "Dzip1l"
## [1749] "Stag1" "9630041A04Rik" "Anapc13" "Slco2a1"
## [1753] "Rab6b" "Topbp1" "Gm5372" "Acad11"
## [1757] "Mrpl3" "Rwdd1" "Twf2" "Tlr9"
## [1761] "Poc1a" "Dusp7" "Abhd14b" "Pcbp4"
## [1765] "Rrp9" "Iqcf1" "Iqcf5" "Nprl2"
## [1769] "Nt5dc1" "Zmynd10" "Tusc2" "Hyal2"
## [1773] "Naa80" "Hyal3" "Ifrd2" "Gm57056"
## [1777] "Mon1a" "Mst1r" "Camkv" "Mcmdc2"
## [1781] "Marcks" "Traip" "Gmppb" "Mst1"
## [1785] "Nicn1" "Amt" "Rhoa" "Gpx1"
## [1789] "1700102P08Rik" "BC048562" "Ccdc71" "Gtf3c6"
## [1793] "Lamb2" "Dalrd3" "Prkar2a" "Nckipsd"
## [1797] "Uqcrc1" "Col7a1" "Ucn2" "Pfkfb4"
## [1801] "Shisa5" "Nme6" "Cdk19os" "Cdc25a"
## [1805] "Map4" "Cspg5" "Ccdc12" "Myl3"
## [1809] "Prss42" "Prss45" "Prss46" "Prss50"
## [1813] "Lrrc2" "Cdc40" "1700061E17Rik" "Lrrfip2"
## [1817] "Epm2aip1" "Trank1" "Ubp1" "4930520O04Rik"
## [1821] "C130032M10Rik" "Dync1li1" "Cmtm6" "Osbpl10"
## [1825] "Gpr6" "Gm9487" "Gadl1" "Azi2"
## [1829] "Itga9" "Vill" "Dlec1" "Acaa1a"
## [1833] "Acvr2b" "Exog" "Wdr48" "Fig4"
## [1837] "Slc25a38" "Mobp" "Myrip" "Eif1b"
## [1841] "Gm7229" "Entpd3" "Rpl14" "Trak1"
## [1845] "1700048O20Rik" "Snrk" "Smpd2" "Mir138-1"
## [1849] "Topaz1" "Zkscan7" "Zfp105" "Kif15"
## [1853] "Tmem42" "Limd1" "4930433N12Rik" "Gm5362"
## [1857] "Aasdhppt" "Cep57l1" "Gria4" "Dync2h1"
## [1861] "Birc2" "Birc3" "Cfap300" "Arhgap42"
## [1865] "Endod1" "Amotl1" "1700012B09Rik" "Mif"
## [1869] "Armc2" "Med17" "Deup1" "Fat3"
## [1873] "Naalad2" "Zfp558" "Muc16" "Or1m1"
## [1877] "Uba52" "Zfp26" "Zfp426" "Foxo3"
## [1881] "Zfp266" "Fbxl12" "Olfm2" "Col5a3"
## [1885] "Eif3g" "Dnmt1" "S1pr2" "Fdx2"
## [1889] "Cdc37" "S1pr5" "Cspp1" "Mtres1"
## [1893] "Kri1" "Cdkn2d" "Mir199a-1" "Spc24"
## [1897] "Kank2" "Dock6" "Gm45914" "Epor"
## [1901] "Rgl3" "Odad3" "Qrsl1" "Zfp653"
## [1905] "Ecsit" "Zfp599" "Zfp810" "Anln"
## [1909] "Rp9" "Gm55908" "Dpy19l1" "Dpy19l2"
## [1913] "Glb1l2" "Lin28b" "Acad8" "Vps26b"
## [1917] "Jam3" "Ntm" "Gm29724" "St14"
## [1921] "Aplp2" "Tmem45b" "Barx2" "Dcps"
## [1925] "Grik2" "Foxred1" "Fam118b" "Hyls1"
## [1929] "Gm6762" "Gm3428" "Chek1" "Stt3a"
## [1933] "Pknox2" "Slc37a2" "Nrgn" "Gprc6a"
## [1937] "Tbrg1" "AW551984" "Or10d5" "Or10d5j"
## [1941] "Or10d5b" "Gramd1b" "Jhy" "Crtam"
## [1945] "Ubash3b" "Gm25401" "4933411G06Rik" "Sorl1"
## [1949] "Grik4" "Oaf" "Rnf26" "Gm10687"
## [1953] "Nlrx1" "Hinfp" "C2cd2l" "Hmbs"
## [1957] "Vps11" "Gopc" "Myl6" "Cenatac"
## [1961] "Foxr1" "Upk2" "Gm47204" "Phldb1"
## [1965] "Arcn1" "Tmem25" "Atp5mg" "Cd3e"
## [1969] "Zfa-ps" "Gm10684" "Cep164" "Gm7286"
## [1973] "Rnf214" "Tagln" "Pafah1b2" "4931429L15Rik"
## [1977] "Gm10677" "Nxpe2" "Rexo2" "Cep85l"
## [1981] "Nnmt" "Htr3b" "Ncam1" "Pts"
## [1985] "Tex12" "Sdhd" "Nkapd1" "Dlat"
## [1989] "Dixdc1" "2310030G06Rik" "Fam184a" "Hspb2"
## [1993] "Sik2" "Hoatz" "Fdx1" "Zc3h12c"
## [1997] "AI593442" "Ddx10" "Atm" "Acat1"
## [2001] "Cul5" "A830018L16Rik" "Tbc1d32" "Tnfaip8l3"
## [2005] "Cyp19a1" "Gldnos" "Dmxl2" "Cib2"
## [2009] "Acsbg1" "Skic8" "Chrnb4" "Etfa"
## [2013] "4930563M21Rik" "Rps8" "Tspan3" "Peak1"
## [2017] "Cimap1c" "Gm10658" "Commd4" "1700017B05Rik"
## [2021] "Ppcdc" "Scamp5" "Lman1l" "Csk"
## [2025] "Edar" "Ccdc33" "Islr" "Islr2"
## [2029] "Tbc1d21" "Cd276" "Neo1" "Bbs4"
## [2033] "Tmem202" "Senp8" "Btf3-ps2" "Oit3"
## [2037] "Nr2e3" "Thsd4" "Gm10655" "Kif23"
## [2041] "Paqr5" "Glce" "Skor1" "Map2k5"
## [2045] "2300009A05Rik" "Smad6" "Mcu" "Dis3l"
## [2049] "Rab11a" "Slc24a1" "Hacd3" "Ankdd1a"
## [2053] "Plekho2" "Zfp609" "Trip4" "Snx1"
## [2057] "Usp3" "Ddit4" "Aph1b" "Ppp1r2"
## [2061] "Aph1c" "Rab8b" "Lactb" "Tpm1"
## [2065] "Tln2" "M5C1000I18Rik" "C2cd4a" "Foxb1"
## [2069] "Anapc16" "Gcnt3" "Rnf111" "Mindy2"
## [2073] "Lipc" "Polr2m" "Myzap" "Cgnl1"
## [2077] "Tex9" "Pigb" "Unc13c" "Cdh23"
## [2081] "Tmod3" "Tmod2" "Gm3671" "Gm54715"
## [2085] "Mlip" "Lrrc1" "Fbxo9" "Rn7sk"
## [2089] "Ooep" "4930542C12Rik" "Slc29a3" "Slc17a5"
## [2093] "Col12a1" "Cox7a2" "Filip1" "Htr1b"
## [2097] "Lca5" "Tent5a" "Gm22830" "Ube3d"
## [2101] "Pgm3" "Pldi" "Cep162" "Tbx18"
## [2105] "Slc25a40" "Syncrip" "Snhg5" "Tmed3"
## [2109] "Tbc1d2b" "Zic1" "Dipk2a" "Chst2"
## [2113] "Kcnb2" "Sgpl1" "Trpc1" "Pls1"
## [2117] "1700065D16Rik" "Nyx" "Rasa2" "E030011O05Rik"
## [2121] "Pxylp1" "Spsb4" "Clstn2" "4930579K19Rik"
## [2125] "Adamts14" "Mrps22" "Gm5920" "Foxl2os"
## [2129] "Gm1123" "Pik3cb" "Faiml" "Mras"
## [2133] "Cldn18" "Sox14" "Il20rb" "Pald1"
## [2137] "Nck1" "Pccb" "Ppp2r3a" "Gm5161"
## [2141] "Ephb1" "Cep63" "Srprb" "Trf"
## [2145] "Inhca" "Tmem108" "Eif4ebp2" "Uba5"
## [2149] "Dnajc13" "Acp3" "Nudt16" "Nudt16l2"
## [2153] "Atp2c1" "Gm7436" "Rpl10" "Col6a6"
## [2157] "Col6a5" "Macroh2a2" "Col6a4" "Ppm1m"
## [2161] "Alas1" "Abhd14a" "Gpr62" "Iqcf3"
## [2165] "Iqcf4" "Grm2" "Tex264" "Rbm15b"
## [2169] "Col13a1" "Dock3" "Mapkapk3" "Hemk1"
## [2173] "Cyb561d2" "Lsmem2" "Sema3b" "Sema3f"
## [2177] "Rbm6" "Rnf123" "Dag1" "Fam241b"
## [2181] "Tcta" "Klhdc8b" "Wdr6" "Gm7628"
## [2185] "Fbxw18" "3000002C10Rik" "Camp" "Ptpn23"
## [2189] "Nradd" "Nbeal2" "Supv3l1" "Pth1r"
## [2193] "Tmie" "Rtp3" "Mlh1" "Mir128-2"
## [2197] "Pdcd6ip" "Gm29825" "Crtap" "Trim71"
## [2201] "Cnot10" "Vps26a" "Gm7780" "Gm5921"
## [2205] "Zcwpw2" "Cmc1" "Plcd1" "Slc22a13"
## [2209] "Slc22a13b" "Scn5a" "Gorasp1" "Csrnp1"
## [2213] "Srgn" "Gm5922" "Gm56077" "Cck"
## [2217] "Lyzl4" "Hhatl" "Ccdc13" "Pomgnt2"
## [2221] "Ano10" "Gm26797" "Zfp445" "Itch"
## [2225] "Terf1" "Ddx21" "1110059G10Rik" "Gm9856"
## [2229] "Tmem158" "Slc6a20a" "Lztfl1" "Fyco1"
## [2233] "mt-Co2" "mt-Tq" "mt-Ts1" "mt-Tp"
## [2237] "Ddx50" "Tarm1" "Maml2" "Or10h1"
## [2241] "Taf1a" "Dhrsx" "Hhipl2" "Tcstv7a"
## [2245] "A730008H23Rik" "Brox" "Disp1" "Stox1"
## [2249] "Mia3" "Ccl28" "n-R5s2" "Dgkk"
## [2253] "Gm14379" "Foxp3" "Syp" "Gpkow"
## [2257] "Praf2" "Smt3h2-ps" "Hnrnph3" "Tfe3"
## [2261] "Gripap1" "Otud5" "Pim2" "Slc35a2"
## [2265] "Timm17b" "Pcsk1n" "Gm7079" "Slc38a5"
## [2269] "4930402K13Rik" "Mypn" "Xk" "H2ap"
## [2273] "H2al3" "Sytl5" "Mid1ip1" "Atp6ap2"
## [2277] "AA414768" "Cypt1" "Maoa" "Dusp21"
## [2281] "Reep3" "Kdm6a" "Rp2" "Jade3"
## [2285] "Rbm10" "Cdk16" "Araf" "Spaca5"
## [2289] "Gm5124" "Gm9439" "Slc6a14" "Zfp365"
## [2293] "Ppp1r2-ps7" "Wdr44" "Tesl1" "Dock11"
## [2297] "Il13ra1" "Pgrmc1" "Rpl7-ps9" "Ube2a"
## [2301] "Rhox6" "Rhox7a" "Arid5b" "Rhox13"
## [2305] "Zbtb33" "Xiap" "Stag2" "Tex13c1"
## [2309] "Prr32" "Actrt1" "Ocrl" "Utp14a"
## [2313] "Bcorl1" "Cabcoco1" "Slc25a14" "Rbmx2"
## [2317] "Gm14719" "Stk26" "Ccdc160" "Phf6"
## [2321] "Hprt1" "Pabir3" "Rtl8c" "Ct55"
## [2325] "Cdk1" "Smim10l2a" "Ints6l" "Slc9a6"
## [2329] "Brs3" "Htatsf1" "Vgll1" "Magea13"
## [2333] "Gm715" "Magec2" "Magea9" "Gm7634"
## [2337] "Gm47211" "Ctag2" "Fmr1" "Fmr1nb"
## [2341] "Aff2" "Gm16407" "Gm8410" "Mamld1"
## [2345] "Mtm1" "Mtmr1" "Vma21" "Gm18636"
## [2349] "Nsdhl" "Zfp185" "Pnma3" "F8a"
## [2353] "Bgn" "Dusp9" "Abcd1" "Gm25226"
## [2357] "Ssr4" "Gm23615" "Bicc1" "Avpr2"
## [2361] "Tktl1" "Emd" "Snora70" "Tafazzin"
## [2365] "Atp6ap1" "Fam50a" "Gm6881" "Gm15362"
## [2369] "Gm4989" "Tfam" "Dkc1" "Brcc3"
## [2373] "Vbp1" "Oat-rs1" "Gm5397" "Cldn34b4"
## [2377] "Tbl1x" "4930480E11Rik" "Gm8754" "Fam47c"
## [2381] "Ube2d1" "Gm8770" "Tmem47" "Fthl17a"
## [2385] "Tab3" "Samt3" "Nr0b1" "Ppp4r3c-ps"
## [2389] "Gm6027" "Gm14773" "Gm5941" "Cisd1"
## [2393] "Arx" "Gm9009" "Gspt2" "Rpl13-ps5"
## [2397] "Pfn5" "Msn" "Gm9062" "Ar"
## [2401] "Yipf6" "Stard8" "Gm4797" "Efnb1"
## [2405] "Igbp1" "Kif4" "Gdpd2" "Gm9078"
## [2409] "Med12" "Nono" "Taf1" "Ogt"
## [2413] "Pin4" "1700049L16Rik" "Gm9109" "Dmrtc1b"
## [2417] "Chic1" "Tsx" "Zcchc13" "Pbdc1"
## [2421] "Cypt2" "Fgf16" "Tbx22" "Tent5d"
## [2425] "Gm6419" "Sh3bgrl" "Cylc1" "Tex16"
## [2429] "Zfp711" "Ube2dnl1" "Ube2dnl2" "Gm5943"
## [2433] "Cpxcr1" "Gm16373" "Gm14926" "Rsph14"
## [2437] "Pabpc5" "Gm4993" "Gm14942" "Gm382"
## [2441] "4921511C20Rik" "Mdm4-ps" "Diaph2" "Srpx2"
## [2445] "Arl13a" "Tmem35a" "Tmem70" "Gucd1"
## [2449] "Cenpi" "Gm16410" "Rpl36a" "Hnrnph2"
## [2453] "Pramex2" "Bhlhb9" "Arxes2" "Tceal9"
## [2457] "Bex3" "Nsa2-ps2" "Lrrc75b" "Tceal1"
## [2461] "BC065397" "Zcchc18" "Fam199x" "Gm15043"
## [2465] "Nrk" "4930513O06Rik" "4933428M09Rik" "Pwwp3b"
## [2469] "Radx" "Susd2" "Rnf128" "Tbc1d8b"
## [2473] "Prps1" "Mid2" "Vsig1" "Col4a5"
## [2477] "Nxt2" "Gm7123" "Gm15031" "Tmem164"
## [2481] "Ddt" "Pak3" "Mir680-2" "Trpc5os"
## [2485] "Mir448" "Alas2" "Pfkfb1" "Fgd1"
## [2489] "Phf8" "Gm15191" "Hsd17b10" "Gstt3"
## [2493] "Smc1a" "Kdm5c" "Ubqln2" "Cypt3"
## [2497] "Amd-ps1" "Acot9" "Smpx" "Klhl34"
## [2501] "Gm8659" "Rps6ka3" "Gstt1" "Eif1ax"
## [2505] "Map7d2" "Gm54697" "Bclaf3" "Sh3kbp1"
## [2509] "Gm8682" "Phka2" "Scml2" "Gm15204"
## [2513] "Rbbp7" "Gstt2" "Gm16459" "Ctps2"
## [2517] "Ap1s2" "Pir" "Vegfd" "Piga"
## [2521] "Asb9" "Gm8580" "Gm7209" "Gm15246"
## [2525] "Smarcb1" "Mid1" "Ezhip" "Ccnb3"
## [2529] "Usp27x" "2010204K13Rik" "Ppp1r3f" "Plp2"
## [2533] "Ccdc120" "Pqbp1" "Gata1" "Mmp11"
## [2537] "Suv39h1" "Wdr13" "Tbc1d25" "Ebp"
## [2541] "Ftsj1" "Ssxb3" "Dynlt3" "Rpgr"
## [2545] "Gm14480" "Gm14473" "Slc5a4b" "Gm14485"
## [2549] "1810030O07Rik" "Med14" "Cask" "Ppp1r2-ps9"
## [2553] "Gm25207" "Gm23516" "Maob" "Efhc2"
## [2557] "Fundc1" "Gdap1" "Prmt2" "Tex13c3"
## [2561] "Ndufb11" "Syn1" "Cfp" "Elk1"
## [2565] "Akap17b" "Septin6" "Rpl39" "Upf3b"
## [2569] "Akap14" "Pcnt" "Ndufa1" "Gm9"
## [2573] "Rhox1" "Rhox8" "Rhox9" "Btg1c"
## [2577] "Tmem255a" "Lamp2" "Cul4b" "C1galt1c1"
## [2581] "Col6a2" "Gm7189" "Gm5385" "Gm14613"
## [2585] "Gm5135" "Dcaf12l2" "Dcaf12l1" "Gm14652"
## [2589] "Gm4987" "Smarca1" "Apln" "Col6a1"
## [2593] "Zdhhc9" "Elf4" "Aifm1" "Zfp280c"
## [2597] "Enox2" "Firre" "Rap2c" "Mbnl3"
## [2601] "Usp26" "Magea14" "Pcbp3" "Gm6402"
## [2605] "Gm7851" "Plac1" "Pabir2" "Mospd1"
## [2609] "AW822252" "1700013H16Rik" "Atf1-ps" "Gm35586"
## [2613] "Gm773" "Slx9" "Ct45a" "Mmgt1"
## [2617] "Map7d3" "Arhgef6" "Rbmx" "Mir504"
## [2621] "Mcf2" "Atp11c" "Mir505" "Gm4909"
## [2625] "Krtap12-24" "Sox3" "Sms" "Gm14676"
## [2629] "4933436I01Rik" "Ids" "Gm14725" "Gm14724"
## [2633] "Cd99l2" "Gabre" "Magea10" "Lrrc3"
## [2637] "Haus7" "Bcap31" "Idh3g" "Hcfc1"
## [2641] "Flna" "Lage3" "Gm44504" "Fam3a"
## [2645] "G6pdx" "Pls3" "Pfkl" "Prkx"
## [2649] "Prrg1" "Gm8761" "Gm5939" "Cfap47"
## [2653] "Mageb16-ps1" "Srsf19" "Gk" "Mageb4"
## [2657] "Gm5759" "Aire" "Dcaf8l" "Fth1-ps"
## [2661] "Gm16465" "Mageb18" "Pdk3" "Zfx"
## [2665] "Eif2s3x" "Gm7061" "Gm14830" "Gm371"
## [2669] "Crispld1" "Gatd3a" "Asb12" "Zc4h2"
## [2673] "1700010D01Rik" "Las1l" "Ophn1" "Gm5760"
## [2677] "Pja1" "P2ry4" "Pdzd11" "Gm14866"
## [2681] "Rrp1" "Tex11" "Snx12" "Gm614"
## [2685] "Zmym3" "Gm4779" "Ercc6l" "Cited1"
## [2689] "Phka1" "1700031F05Rik" "Dmrtc1a" "Pdxk"
## [2693] "Cop1" "Gm9785" "Abcb7" "Rpl12"
## [2697] "Atrx" "Magt1" "Fndc3c1" "Itm2a"
## [2701] "Chmp1b2" "Wmp" "Tektl1" "Gm379"
## [2705] "Brwd3" "Hmgn5" "Rps6ka6" "Hdx"
## [2709] "Satl1" "Chm" "Gm5942" "Gm14911"
## [2713] "Dmtf1l" "2610008E11Rik" "Cldn34c4" "Gm7820"
## [2717] "Tspan6" "Trmt2b" "Taf7l" "Gla"
## [2721] "Gm7855" "Gm10344" "Armcx2" "Zmat1"
## [2725] "Plpp2" "Tcp11x2" "Tmsb15a" "Nxf3"
## [2729] "Tceal8" "Tceal5" "Esx1" "Gm8036"
## [2733] "Tex13a" "Ripply1" "Nup62cl" "Mier2"
## [2737] "Tsc22d3" "Psmd10" "Acsl4" "Gm4995"
## [2741] "Chrdl1" "Capn6" "Maged2" "Gnl3l"
## [2745] "Tsr2" "A230072E10Rik" "C2cd4c" "Gm4919"
## [2749] "Ribc1" "Shroom2" "Gm7150" "Samt2b"
## [2753] "Cldn34b2" "Gm4997" "Sat1" "Ptchd1"
## [2757] "Gm7312" "Polrmt" "Suclg2" "Phex"
## [2761] "Gm15173" "Gm8644" "Cnksr2" "Gm15190"
## [2765] "Pdha1" "Ppef1" "Cdkl5" "Gja6"
## [2769] "Plppr3" "Reps2" "Txlng" "Rnf138rt1"
## [2773] "Zrsr2" "Car5b" "Siah1b" "Mospd2"
## [2777] "Ofd1" "Rab9" "Gm15229" "Il17a"
## [2781] "Med16" "Tmsb4x" "Prps2" "Gm6744"
## [2785] "Hccs" "Vamp7" "Uba1y" "Kdm5d"
## [2789] "Eif2s3y" "Uba1y-ps2" "Zfy1" "R3hdm4"
## [2793] "Uty" "Ddx3y" "Usp9y" "Zfy2"
## [2797] "Sry" "Gm28649" "Srsy" "4932431L22Rik"
## [2801] "Gm29276" "Gm20826" "Polr2e" "Krt85"
## [2805] "Mrgpra4" "Zfp1006" "Dynll1" "Rn18s-rs5"
## [2809] "Gm20939" "Snrnp40" "Noc2l" "2310009B15Rik"
## [2813] "Fam90a1a" "Sbno2" "Ankrd63" "Samd11"
## [2817] "Plekhn1" "Ccdc82" "Gm7073" "Cbarp"
## [2821] "Gamt" "2310011J03Rik" "Pcsk4" "Adamtsl5"
## [2825] "Mex3d" "Paqr8" "Uqcr11" "Btbd2"
## [2829] "Mknk2" "Plekhj1" "Jsrp1" "Lsm7"
## [2833] "Timm13" "Lmnb2" "Gng7" "Diras1"
## [2837] "Efhc1" "Slc39a3" "Sgta" "Mrpl54"
## [2841] "Tjp3" "Gipc3" "Hmg20b" "Tektip1"
## [2845] "Fzr1" "Nfic" "Celf5" "Gsta3"
## [2849] "Ncln" "S1pr4" "Gna11" "Sirt6"
## [2853] "Zfp938" "Spata31h1" "Uqcc6" "Glt8d2"
## [2857] "Nfyb" "Slc41a2" "B3gat2" "Aldh1l2"
## [2861] "Ckap4" "Mterf2" "Cry1" "Gm6714"
## [2865] "Prdm4" "Rtcb" "A230060F14Rik" "Ascl1"
## [2869] "Parpbp" "Rab7" "Col9a1" "Dram1"
## [2873] "Chpt1" "Utp20" "Gas2l3" "Slc17a8"
## [2877] "Actr6" "Apaf1" "Slc25a3" "Tmpo"
## [2881] "Cfap54" "Lmbrd1" "Snrpf" "Vezt"
## [2885] "Cradd" "Socs2" "Mrpl42" "Anapc15"
## [2889] "Gm20091" "Gm8613" "Csl" "Tmtc3"
## [2893] "Gm19028" "Rlig1" "Alx1" "Tmtc2"
## [2897] "Gm48298" "Acss3" "Myf5" "Myf6"
## [2901] "Ptprq" "Brcc3dc" "Nav3" "Dnaaf6rt"
## [2905] "Zdhhc17" "Gm47866" "Trhde" "Gm55666"
## [2909] "Tbc1d15" "Rab21" "Thap2" "Taf7l2"
## [2913] "Kcnmb4" "Gm5781" "Alyreffm2" "Frs2"
## [2917] "Yeats4" "Lyz2" "Lyz1" "Mdm2"
## [2921] "Nup107" "Rap1b" "Cdc5l" "Dyrk2"
## [2925] "Irak3" "1700001G17Rik" "Rassf3" "Tbk1"
## [2929] "Xpot" "Srgap1" "Rxylt1" "Mirlet7i"
## [2933] "Atp23" "Tsfm" "Tspan31" "Os9"
## [2937] "Rab23" "Slc26a10" "Arhgef25" "Pip4k2c"
## [2941] "Kif5a" "Mbd6" "Mars1" "Gli1"
## [2945] "Shmt2" "Lrp1" "Nab2" "Dst"
## [2949] "Rbms2" "Coq10a" "Slc39a5" "Nabp2"
## [2953] "Myl6b" "Zc3h10" "Pa2g4" "Ikzf4"
## [2957] "Suox" "Rpsa" "Imp4" "Ormdl2"
## [2961] "Or6c8b" "Or6c8" "Or6c201" "Or10p1"
## [2965] "Or6c69b" "Vmn2r86" "Pisd-ps1" "Eif4enif1"
## [2969] "Pla2g3" "Cfc1" "Selenom" "Dusp18"
## [2973] "Pes1" "Gal3st1" "Gm11954" "Sec14l4"
## [2977] "Sec14l3" "Sf3a1" "Castor1" "Zmat5"
## [2981] "Canx" "Arhgef4" "Nipsnap1" "Thoc5"
## [2985] "Ap1b1" "Gm30172" "Xbp1" "Ankrd48"
## [2989] "Dbnl" "Aebp1" "Ykt6" "Gm11401"
## [2993] "Plekhb2" "Gm11971" "Ccm2" "Ramp3"
## [2997] "Adcy1" "Gm11992" "Gm11996" "Spmip7"
## [3001] "Gm12009" "Gm12011" "Vstm2a" "Hs6st1"
## [3005] "Akt2" "Egfr" "Ppp3r1" "Dnaaf10"
## [3009] "Glul" "Spred2" "Rab1a" "Peli1"
## [3013] "Gm24917" "Zrsr2-ps1" "Fer1l5" "Cct4"
## [3017] "Fam161a" "Xpo1" "1700030C12Rik" "Pus10"
## [3021] "Bcl11a" "4933427E13Rik" "Fancl" "Efemp1"
## [3025] "Pnpt1" "Cnnm4" "Ccdc88a" "Clhc1"
## [3029] "Gm8098" "Asb3" "Cpeb4" "4930524B15Rik"
## [3033] "Gm12109" "Snrnp25" "Mpg" "Stk10"
## [3037] "Cnnm3" "Fbxw11" "Ssbp1" "D130052B06Rik"
## [3041] "Insyn2b" "Slit3" "Gm12129" "Nudcd2"
## [3045] "Btf3-ps7" "Atp10b" "Slu7" "Zap70"
## [3049] "Pwwp2a" "Rnf145" "Clint1" "Adam19"
## [3053] "Garin3" "Med7" "Gm12176" "Gm12181"
## [3057] "Rack1" "Snord95" "Vwa3b" "Trim7"
## [3061] "Or2t26" "Or2o1" "Zfp62" "Or2y1g"
## [3065] "Or2y1f" "Or2y1b" "Or2y13" "Flt4"
## [3069] "Tbc1d9b" "Cnga3" "Mrnip" "Mgat4b"
## [3073] "Cby3" "Hnrnph1" "Adamts2" "Grm6"
## [3077] "Gm12201" "Col23a1" "Nhp2" "D930048N14Rik"
## [3081] "Inpp4a" "Sar1b" "Gm26061" "Skp1"
## [3085] "9530068E07Rik" "Fstl4" "Gdf9" "Shroom1"
## [3089] "Gm9945" "Septin8" "Kif3a" "Cpsf7"
## [3093] "Unc50" "Irf1" "P4ha2" "Gm12221"
## [3097] "Gm12222" "Acsl6" "Meikin" "Fnip1"
## [3101] "Hint1" "Gpx3" "Zic5" "Lipt1"
## [3105] "Mfap3" "Galnt10" "Cnot8" "Mrpl22"
## [3109] "Zfp692" "Sh3bp5l" "Trim58" "Or2ak7"
## [3113] "Or2ak4" "Or2t45" "Pdcl3" "Or2t44"
## [3117] "Or9e1" "2810021J22Rik" "Btnl10" "H2bc27"
## [3121] "H3f4" "Trim11" "Gm10435" "2310033P09Rik"
## [3125] "Wnt9a" "Npas2" "4933439C10Rik" "Gm16062"
## [3129] "Nt5m" "Med9" "Rai1" "Drc3"
## [3133] "Drg2" "Llgl1" "Mief2" "Smcr8"
## [3137] "Cnot11" "Dhrs7b" "Kcnj12" "Tnfrsf13b"
## [3141] "Aldh3a1" "Mfap4" "B9d1" "Fam83g"
## [3145] "Specc1" "Adora2b" "Ttc19" "Map4k4"
## [3149] "Pigl" "Trpv2" "Snord49a" "Mmgt2"
## [3153] "Tvp23b" "Cdrt4" "Tekt3" "Pmp22"
## [3157] "Elac2" "Gm53042" "Il1r1" "Zkscan6"
## [3161] "Pirt" "Tmem220" "Gas7" "Gsg1l2"
## [3165] "Dhrs7c" "Stx8" "Pik3r6" "Mfsd6l"
## [3169] "Ccdc42" "Slc9a2" "Myh10" "Rnf222"
## [3173] "Rpl26" "Slc25a35" "Aurkb" "Borcs6"
## [3177] "Tmem107" "Vamp2" "Per1" "Hes7"
## [3181] "Tmem182" "Aloxe3" "Trappc1" "Kcnab3"
## [3185] "Rnf227" "Chd3" "Trp53" "Sat2"
## [3189] "Fxr2" "Sox15" "Zbtb4" "Mrps9"
## [3193] "G630025P09Rik" "Plscr3" "Gps2" "Cldn7"
## [3197] "Ctdnep1" "Gabarap" "Phf23" "Dvl2"
## [3201] "Asgr2" "Slc16a11" "Psph" "AI597479"
## [3205] "Mir497" "Mir195a" "Med11" "Zmynd15"
## [3209] "Tm4sf5" "Psmb6" "Mink1" "Rnf167"
## [3213] "Eno3" "Kif1c" "Nck2" "Zfp3"
## [3217] "Rabep1" "Rpain" "Mis12" "Wscd1"
## [3221] "Pimreg" "Txndc17" "4930563E22Rik" "Ggt6"
## [3225] "Mybbp1a" "Ecrg4" "Ankfy1" "Ncbp3"
## [3229] "Itgae" "P2rx5" "Shpk" "Trpv1"
## [3233] "Spata22" "Or1e17" "Or3a1b" "Or3a1c"
## [3237] "Gm19587" "Ccdc92b" "Cluh" "Mettl16"
## [3241] "Tsr1" "Smg6" "Mir212" "Mir132"
## [3245] "Rtn4rl1" "Rilp" "Scarf1" "Ercc5"
## [3249] "Myo1c" "Crk" "Tlcd3a" "Dbil5"
## [3253] "Mrm3" "Bhlha9" "Trarg1" "Tmigd1"
## [3257] "Slc6a4" "Ssh2" "Col3a1" "Git1"
## [3261] "Gm11191" "Myo18a" "Sez6" "Phf12"
## [3265] "Dhrs13" "Flot2" "Fam222b" "Proca1"
## [3269] "Sdf2" "Wdr75" "Rskr" "Spag5"
## [3273] "Aldoc" "Pigs" "Unc119" "Slc46a1"
## [3277] "Vtn" "Sebox" "Ift20" "Lyrm9"
## [3281] "Dnah7b" "Gm11201" "Rab11fip4" "Mir193a"
## [3285] "Mir365-2" "Atad5" "Rhot1" "Rhbdl3"
## [3289] "Zfp207" "Cdk5r1" "Tmem98" "n-R5s211"
## [3293] "Spaca3" "Tmem132e" "Gm11426" "Zfp830"
## [3297] "1700020L24Rik" "Taf15" "E230016K23Rik" "Ccl4"
## [3301] "Wfdc17" "Wfdc21" "Gm8357" "Ddx52"
## [3305] "Synrg" "Ggnbp2os" "Myo19" "Chct1"
## [3309] "Tbx2" "Tbx4" "Brip1os" "Rnft1"
## [3313] "Tubd1" "Ube2r2" "Gm8384" "Ptrh2"
## [3317] "Ska2" "Trim37" "Rnf43" "Mks1"
## [3321] "Srsf1" "Vezf1" "Mrps23" "2210409E12Rik"
## [3325] "Coil" "Stat1" "Trim25" "Dgkeos"
## [3329] "Cox11" "Gm11502" "Tob1" "Ankrd40"
## [3333] "Spata20" "Lrrc59" "Mrpl27" "Cdc34b"
## [3337] "Nemp2" "Col1a1" "Ppp1r9b" "Slc35b1"
## [3341] "B130006D01Rik" "Phospho1" "Gngt2" "Gip"
## [3345] "Snf8" "Hoxb9" "Hoxb8" "Hibch"
## [3349] "Hoxb7" "Hoxb3" "Hoxb1" "Copz2"
## [3353] "Prr15l" "Scrn2" "Osbpl7" "Mrpl45"
## [3357] "Socs7" "Arhgap23" "Ormdl1" "Psmb3"
## [3361] "Lasp1" "B230217C12Rik" "Cdk12" "Ppp1r1b"
## [3365] "Erbb2" "Grb7" "Lrrc3c" "Gsdma3"
## [3369] "Gsdma" "Osgepl1" "Csf3" "Msl1"
## [3373] "Casc3" "Wipf2" "Cdc6" "Rara"
## [3377] "Igfbp4" "Krtap31-3" "Gm11560" "Eif1"
## [3381] "Ccdc150" "Gast" "Fkbp10" "Odad4"
## [3385] "Cnp" "Hspb9" "Atp6v0a1" "Naglu"
## [3389] "Coasy" "Mlx" "Tubg1" "Mob4"
## [3393] "Tubg2" "Ramp2" "Vps25" "Cntd1"
## [3397] "Aoc2" "Rnd2" "Tmem106a" "Rdm1"
## [3401] "Arl4d" "4930417O22Rik" "Mars2" "Cfap97d1"
## [3405] "Cd300lg" "Ppih" "Nags" "Hrob"
## [3409] "Tmub2" "Rundc3a" "Grn" "Mdk-ps1"
## [3413] "Adam11" "Rps24" "Hexim2" "Fmnl1"
## [3417] "Wnt3" "Arf2" "Myl4" "Itgb3"
## [3421] "Efcab3" "Tlk2" "Mrc2" "Tanc2"
## [3425] "Smim7" "1700066M21Rik" "Gm9910" "Ace"
## [3429] "Kcnh6" "Map3k3" "Prr29" "Snord104"
## [3433] "Cep95" "Psmd12" "Apoh" "Gm11667"
## [3437] "Maip1" "Cep112" "Axin2" "9930022D16Rik"
## [3441] "Prkar1a" "Gm11675" "Sox9" "4933434M16Rik"
## [3445] "Cog1" "Mtnap1" "Gm11691" "Sgo2a"
## [3449] "Ttyh2" "Dnai2" "Kif19a" "Gprc5c"
## [3453] "Cd300a" "Nherf1" "Tmem104" "Cdr2l"
## [3457] "Mrpl58" "Kctd2" "Aox3" "Trim80"
## [3461] "Armc7" "Nup85" "Mrps7" "Gm23699"
## [3465] "Tsen54" "Llgl2" "Myo15b" "Erln"
## [3469] "Sap30bp" "Aox4" "Itgb4" "Unk"
## [3473] "Ten1" "Rps11-ps2" "Sphk1" "Prcd"
## [3477] "BC018473" "Mettl23" "Septin9" "6030468B19Rik"
## [3481] "Ndufb3" "Afmid" "Birc5" "Tmem235"
## [3485] "Socs3" "Pgs1" "Engase" "Enpp7"
## [3489] "Cbx2" "Ccdc40" "Gaa" "Cflar"
## [3493] "Slc26a11" "Rnf213" "Endov" "Chmp6"
## [3497] "Baiap2" "0610009L18Rik" "Fscn2" "Ccdc137"
## [3501] "Hgs" "Mrpl12" "Casp8" "Slc25a10"
## [3505] "Gcgr" "Anapc11" "Npb" "Lrrc45"
## [3509] "Uts2r" "Hexd" "Narf" "Foxk2"
## [3513] "Fn3krp" "G730003C15Rik" "Tbcd" "Ptchd3"
## [3517] "Sfi1" "Limk2" "Rnf185" "Smtn"
## [3521] "Tug1" "Osbp2" "Tcn2" "Sec14l2"
## [3525] "Fzd7" "Gm11956" "Uqcr10" "Nf2"
## [3529] "Nefh" "Gas2l1" "Ewsr1" "Emid1"
## [3533] "Kremen1" "Znrf3" "Ccdc117" "Polr2f"
## [3537] "Gm973" "Mrps24" "Urgcp" "Pgam2"
## [3541] "Pold2" "Gck" "Camk2b" "Nudcd3"
## [3545] "Rps15a-ps4" "Npc1l1" "Ddx56" "Fam117b"
## [3549] "H2az2" "Purb" "Nacad" "Gm11979"
## [3553] "Hus1" "Sun3" "Polr2c" "Gm26458"
## [3557] "4930512M02Rik" "Fignl1" "Carf" "Gm25058"
## [3561] "Cobl" "Sec61g" "Ublcp1" "Gm12664"
## [3565] "Pno1" "Gm12015" "Etaa1" "Gm12020"
## [3569] "Meis1" "Nbeal1" "Actr2" "Aftph"
## [3573] "Lgalsl" "Ugp2" "4932414J04Rik" "Mdh1"
## [3577] "Otx1" "Gm12058" "Commd1" "1700093K21Rik"
## [3581] "Cyp20a1" "Selenok-ps1" "Pex13" "Papolg"
## [3585] "A830031A19Rik" "5730522E02Rik" "6820445E23Rik" "Vrk2"
## [3589] "Cyb5d1" "Cfap36" "Fem1al" "Abi2"
## [3593] "Cimip6" "Acyp2" "Stc2" "Bod1"
## [3597] "Il9r" "Rhbdf1" "Nprl3" "Efcab9"
## [3601] "Smim23" "Fgf18" "Eif4a1" "Npm1"
## [3605] "Tlx3" "Ranbp17" "Anp32-ps" "Foxi1"
## [3609] "Dock2" "Rars1" "Wwc1" "Tenm2"
## [3613] "Gm6644" "Pard3b" "Mat2b" "Hmmr"
## [3617] "Ccng1" "Gabra1" "Pttg1" "Gm12151"
## [3621] "Ttc1" "Adra1b" "Thg1l" "Sft2d1"
## [3625] "Gm11599" "Gm12186" "Btnl9" "Cnot6"
## [3629] "Sqstm1" "Rufy1" "Zfp354c" "Zfp354b"
## [3633] "4933414I15Rik" "Msantd5l" "Rmnd5b" "Eef1b2"
## [3637] "N4bp3" "Sec24a" "Jade2" "Or2y7"
## [3641] "Tcf7" "Hspa4" "Leap2" "Uqcrq"
## [3645] "Gm9837" "Il13" "Eif5" "Mir686"
## [3649] "Adam23" "Rad50" "Gm17334" "Slc22a5"
## [3653] "Slc22a4" "Pdlim4" "Lyrm7" "Tnip1"
## [3657] "Anxa6" "Atp5pb" "Slc36a3" "Crygf"
## [3661] "Fat2" "Sparc" "Fam114a2" "Hand1"
## [3665] "Or2z2" "Cfap144" "Zfp39" "H2bc26"
## [3669] "Obscn" "Iba57" "Unc80" "Guk1"
## [3673] "Arf1" "Wnt3a" "Zfp867" "Zkscan17"
## [3677] "Or2b11" "Gm12261" "Pld6" "Rasd1"
## [3681] "Pemt" "Rpe" "4930412M03Rik" "Srebf1"
## [3685] "Tom1l2" "Atpaf2" "Gm12620" "Flii"
## [3689] "Top3a" "Shmt1" "Tmem11" "Map2k3os"
## [3693] "Gm23422" "Usp22" "Slc47a2" "Slc47a1"
## [3697] "Rnf112" "Mapk7" "B9d1os" "Prpsap2"
## [3701] "A530017D24Rik" "Akap10" "Zswim7" "Vwc2l"
## [3705] "Zfp287" "Wsb2-ps" "Zfp286" "Hs3st3b1"
## [3709] "Cox10" "Arhgap44" "Map2k4" "Gm12298"
## [3713] "Adprm" "Glp2r" "Atic" "Usp43"
## [3717] "Ntn1" "Ndel1" "Odf4" "9130213A22Rik"
## [3721] "Cntrob" "Tmem88" "Efnb3" "Wrap53"
## [3725] "Atp1b2" "Xrcc5" "Shbg" "Mpdu1"
## [3729] "Cd68" "Senp3" "Slc35g3" "Nlgn2"
## [3733] "Tnk1" "Kctd11" "Acap1" "2810408A11Rik"
## [3737] "Igfbp2" "Slc2a4" "Acadvl" "Bcl6b"
## [3741] "Rnasek" "Alox12" "Alox15" "Pelp1"
## [3745] "Cxcl16" "Chrne" "Slc25a11" "Gpbar1"
## [3749] "Pfn1" "Spag7" "Inca1" "C1qbp"
## [3753] "Dhx33" "Derl2" "Gm12321" "Nlrp1c-ps"
## [3757] "Med31" "Tekt1" "Hdac5" "Pnkd"
## [3761] "Spns2" "Spns3" "Gm24143" "Haspin"
## [3765] "Emc6" "Ctns" "Or1e21" "Or3a1d"
## [3769] "Rpa1" "Serpinf1" "Catip" "Serpinf2"
## [3773] "Doc2b" "Rph3al" "Vps53" "Gemin4"
## [3777] "Glod4" "Abr" "Gosr1" "Cpd"
## [3781] "Nsrp1" "Slc11a1" "Mir423" "Trp53i13"
## [3785] "Gm10392" "Taok1" "Gm11190" "Dhrs13os"
## [3789] "Eral1" "Lsm6" "Traf4" "Nek8"
## [3793] "Ctdsp1" "Snord42b" "Supt6" "Foxn1"
## [3797] "Tmem199" "Tnfaip1" "Tmem97" "Nlk"
## [3801] "Gm11197" "Ccnq" "Lgals9" "Mir26b"
## [3805] "Ksr1" "Wsb1" "Omg" "Utp6"
## [3809] "Crlf3" "5730455P16Rik" "Myo1d" "Asic2"
## [3813] "Cct6b" "Rad51d" "Bcs1l" "Unc45bos"
## [3817] "Slfn5os" "Pex12" "Mmp28" "Heatr9"
## [3821] "Ccl5" "Rpl9" "Dusp14" "Aatf"
## [3825] "Lhx1" "Cyp27a1" "Mrm1" "Dhrs11"
## [3829] "Pigw" "Appbp2" "Gm57365" "Gm11444"
## [3833] "Ints2" "Rps6kb1" "Gm9975" "Rpl13a"
## [3837] "Wnt6" "Dhx40" "Smg8" "Prr11"
## [3841] "Gm22883" "Epx" "Or4d2b" "Or4d2"
## [3845] "Dynll2" "Akap1" "Scpep1" "Wnt10a"
## [3849] "Elobl" "Dgke" "Ankfn1" "Pctp"
## [3853] "Hlf" "Stxbp4" "Tom1l1" "Utp18"
## [3857] "Nme2" "Nme1" "Cdk5r2" "Rpl27"
## [3861] "Wfikkn2" "Luc7l3" "Mycbpap" "Rsad1"
## [3865] "Eme1" "Xylt2" "Gm11545" "Sgca"
## [3869] "Pdk2" "Atp6v0d1" "Ankzf1" "Itga3"
## [3873] "Nxph3" "Ngfr" "Zfp652os" "Gm11536"
## [3877] "Gm11529" "Snx11" "Nfe2l1" "Cdk5rap3"
## [3881] "Sp2" "Stk16" "Tbkbp1" "4933428G20Rik"
## [3885] "Epop" "Pcgf2" "Pip4k2b" "Spmap1"
## [3889] "Fbxo47" "Plxdc1" "Cacnb1" "Stac2"
## [3893] "Speg" "Fbxl20" "Neurod2" "Mien1"
## [3897] "Ormdl3" "Nr1d1" "Gm12359" "Gjd3"
## [3901] "Ccr7" "Smarce1" "Krt222" "Gmppa"
## [3905] "Krt12" "Krtap3-2" "Krtap3-1" "Krtap1-5"
## [3909] "Krtap1-4" "Krtap1-3" "Krtap9-3" "Krtap4-2"
## [3913] "Krtap4-7" "Krtap4-24" "Asic4" "Krtap4-25"
## [3917] "Krtap4-26" "Krtap17-1" "Krt33b" "Krt34"
## [3921] "Krt31" "Krt42" "Hap1" "Atp5mc1"
## [3925] "Jup" "Stk11ip" "P3h4" "Klhl11"
## [3929] "Dnajc7" "Zfp385c" "Dhx58" "Kat2a"
## [3933] "Rab5c" "Hcrt" "Stat5b" "Stat3"
## [3937] "Slc4a3" "Psmc3ip" "Ccr10" "Coa3"
## [3941] "Aarsd1" "Ptges3l" "Vat1" "Brca1"
## [3945] "Meox1" "Sost" "Mpp3" "Gm5257"
## [3949] "Ppy" "Pyy" "Tmem101" "Atxn7l3"
## [3953] "Ubtf" "Fam171a2" "Gpatch8" "Ccdc43"
## [3957] "Eftud2" "Gfap" "Sgpp2" "Kif18b"
## [3961] "C1ql1" "Dcakd" "Plcd3" "Spata32"
## [3965] "Arhgap27" "Plekhm1" "Lrrc37a" "Lrrc37"
## [3969] "Lyzl6" "Acsl3" "Gosr2" "Wnt9b"
## [3973] "Nsf" "Kansl1" "Cyb561" "Ccdc47"
## [3977] "Ftsj3" "Smarcd2" "Cd79b" "Ern1"
## [3981] "Gm49705" "Kcne4" "Polg2" "Smurf2"
## [3985] "Gm11708" "Nol11" "Cacng1" "Cacng4"
## [3989] "Cacng5" "Prkca" "Slc16a6" "Fam20a"
## [3993] "Nyap2" "Abca5" "Gm11681" "Vcf1"
## [3997] "Cpsf4l" "Sdk2" "4932435O22Rik" "Btbd17"
## [4001] "Cd300e" "Cd300lf" "Nat9" "Rhbdd1"
## [4005] "Fdxr" "Fads6" "Ush1g" "Hid1"
## [4009] "Nt5c" "Jpt1" "Sumo2" "Gga3"
## [4013] "Mif4gd" "Slc25a19" "Gm54925" "Grb2"
## [4017] "Galk1" "Wbp2" "Trim65" "Mrpl38"
## [4021] "Fbf1" "Acox1" "Srp68" "Exoc7"
## [4025] "Foxj1" "Daw1" "Qrich2" "Ube2o"
## [4029] "Cygb" "Mxra7" "Jmjd6" "Srsf2"
## [4033] "Tmc6" "Tk1" "Usp36" "Dnah17"
## [4037] "Fbxo36" "Cyth1" "Timp2" "Lgals3bp"
## [4041] "Cant1" "Rbfox3" "Cbx8" "Cbx4"
## [4045] "Tbc1d16" "Eif4a3" "Nptx1" "Itm2c"
## [4049] "Aatk" "Mir338" "Cep131" "Slc38a10"
## [4053] "Reno1" "Faap100" "Oxld1" "Mcrip1"
## [4057] "Ppp1r27" "P4hb" "4933407L21Rik" "Arhgdia"
## [4061] "Alyref" "Pcyt2" "Sirt7" "Mafg"
## [4065] "Pycr1" "Cenpx" "Dcxr" "Cbr2"
## [4069] "Rfng" "2810459M11Rik" "Dus1l" "Fasn"
## [4073] "Ccdc57" "Tex19.2" "Ogfod3" "Cybc1"
## [4077] "Wdr45b" "Rab40b" "B3gntl1" "Rab10os"
## [4081] "B3gnt7" "Kif3c" "Dtnb" "Dnmt3a"
## [4085] "Ptrhd1" "Sf3b6" "Atad2b" "2810032G03Rik"
## [4089] "Nfyc" "Apob" "Ldah" "Dlg1"
## [4093] "C130036L24Rik" "Sdc1" "Acaca" "Rdh14"
## [4097] "Smc6" "Cyria" "Gm9202" "Ntsr2"
## [4101] "E2f6" "Rock2" "Nol10" "Cops7b"
## [4105] "Odc1" "Gm22748" "Hpcal1" "1700030C10Rik"
## [4109] "Bnip3l" "5730507C01Rik" "2410018L13Rik" "Gm4983"
## [4113] "Gm5784" "9030624G23Rik" "Prss56" "Asap2"
## [4117] "Cpsf3" "Iah1" "Gm49251" "Taf1b"
## [4121] "Klf11" "Rrm2" "Kidins220" "Cmpk2"
## [4125] "Rnaseh1" "Chrng" "Adi1" "Eipr1"
## [4129] "Pxdn" "Tmem18" "Sh3yl1" "Lamb1"
## [4133] "Gm9359" "Gm25913" "Ccdc71l" "Gm18726"
## [4137] "Eif4e2" "Nampt" "Gdap10" "Sypl1"
## [4141] "Atxn7l1" "Efcab10" "Polr1f" "Prps1l1"
## [4145] "Ube2frt" "Ankmy2" "Sostdc1" "Efhd1"
## [4149] "Etv1" "Gm7008" "Gm7242" "Pnpla8"
## [4153] "Rps11-ps4" "G2e3" "Ap4s1" "Gm5785"
## [4157] "Nubpl" "Arhgap5" "Snorc" "Akap6"
## [4161] "Gm47553" "Prorp" "Psma6" "Aldoart2"
## [4165] "Insm2" "Pax9" "Mipol1" "Ttc6"
## [4169] "Gemin2" "Inpp5d" "Pnn" "Mia2"
## [4173] "Gm7719" "Gm30738" "Gm527" "Togaram1"
## [4177] "Prpf39" "Wdr20rt" "Lrr1" "Mgat2"
## [4181] "Atg16l1" "9330151L19Rik" "Klhdc1" "Arf6"
## [4185] "4930512B01Rik" "Gm3086" "Tmx1" "Frmd6"
## [4189] "Gm10457" "Psma3" "Arid4a" "Dgkd"
## [4193] "Tomm20l" "2700049A03Rik" "Dact1" "Daam1"
## [4197] "Jkamp" "Mnat1" "Slc38a6" "Hif1a"
## [4201] "S100a11-ps" "Snapc1" "Tmem216" "Mroh2a"
## [4205] "Rhoj" "Syne2" "Mthfd1" "Akap5"
## [4209] "Ppp1r36" "Ppp1r36dn" "Churc1" "Gm25926"
## [4213] "Ccdc196" "Gphn" "Trpm8" "Eif2s1"
## [4217] "Rad51b" "Exd2" "Slc39a9" "Plekhd1"
## [4221] "Susd6" "Srsf5" "Smoc1" "Ttc9"
## [4225] "Rbm25" "Sh3bp4" "Papln" "Riox1"
## [4229] "Acot2" "Dnal1" "Coq6" "Bbof1"
## [4233] "Rnf113a2" "Lin52" "Isca2" "Fcf1"
## [4237] "Agap1" "Ylpm1" "Dlst" "Eif2b2"
## [4241] "Zc2hc1c" "Jdp2" "Batf" "Flvcr2"
## [4245] "Vash1" "Lrrc74a" "Tmem63c" "Mlph"
## [4249] "Gstz1" "Ahsa1" "Slirp" "Eif1ad18"
## [4253] "Nrxn3" "Tshr" "Gm6869" "Ttc8"
## [4257] "Kcnk13" "Gm10433" "Prlh" "Gm10432"
## [4261] "A630072L19Rik" "D130020L05Rik" "Kif4-ps" "Chga"
## [4265] "Ubr7" "Cox8c" "Fam181a" "Ifi27"
## [4269] "Serpina5" "Scly" "Serpina3a" "Serpina3f"
## [4273] "Serpina3n" "4930408O17Rik" "Glrx5" "Bdkrb2"
## [4277] "Bdkrb1" "Gskip" "Cyp46a1" "Evl"
## [4281] "Espnl" "Mir342" "Yy1" "Mir345"
## [4285] "Slc25a47" "Wdr25" "Mif-ps7" "Dlk1"
## [4289] "Meg3" "Mir673" "Mir337" "Erfe"
## [4293] "Mir665" "6430411K18Rik" "Mir341" "Mir370"
## [4297] "Mir494" "Mir679" "Mir666" "Mir667"
## [4301] "Mir668" "Gm9661" "Traf3ip1" "Ppp2r5c"
## [4305] "Wdr20" "Tecpr2" "Rcor1" "Amn"
## [4309] "Exoc3l4" "Tnfaip2" "Snora28" "Coa8"
## [4313] "Aspg" "Ythdf1" "Asb1" "Kif26a"
## [4317] "A530016L24Rik" "Inf2" "Adss1" "Siva1"
## [4321] "Zbtb42" "Cep170b" "Clba1" "9230104M06Rik"
## [4325] "Pacs2" "Or9s23" "Tex22" "Mta1"
## [4329] "Crip2" "Crip1" "Tedc1" "Adam6a"
## [4333] "Zfp386" "Vipr2" "Esyt2" "Ncapg2"
## [4337] "Or9s15" "Rapgef5" "Cdca7l" "Ncoa4"
## [4341] "Tmem196" "Rab10" "1110002L01Rik" "Rps7-ps2"
## [4345] "Dnmt3aos" "Ncoa1" "Fam228a" "Or9s14"
## [4349] "Fam228b" "Mfsd2b" "Ubxn2a" "Klhl29"
## [4353] "Gm46311" "Gdf7" "Rhob" "Pgk1"
## [4357] "Kcns3" "Msgn1" "Or9s13" "Gen1"
## [4361] "Gm4803" "Rpl21-ps2" "Ddx1" "Gm4929"
## [4365] "Lratd1" "Trib2" "Lpin1" "Greb1"
## [4369] "Cimip5" "Gpr35" "Zfp125" "3110053B16Rik"
## [4373] "Itgb1bp1" "Adam17" "Ywhaq" "Gm19924"
## [4377] "Gm49929" "Gm20472" "Gm16372" "Id2"
## [4381] "Gpc1" "Silc1" "Sox11" "Dcdc2c"
## [4385] "Allc" "Colec11" "Rps7" "Trappc12"
## [4389] "Acp1" "Dld" "Cbll1" "Mir149"
## [4393] "Dus4l" "Hbp1" "Prkar2b" "Pik3cg"
## [4397] "Gm54696" "Hdac9" "Mir680-3" "Ahr"
## [4401] "Tspan13" "Bzw2" "Dusp28" "Lrrc72"
## [4405] "Crppa" "Gm4257" "Ifrd1" "Zfp277"
## [4409] "Nova1" "Gm7172" "Strn3" "Heatr5a"
## [4413] "Dtd2" "Rnpepl1" "Sptssa" "Eapp"
## [4417] "Snx6" "2700097O09Rik" "Gm7511" "Ppp2r3c"
## [4421] "Ralgapa1" "Mbip" "Nkx2-1" "Slc25a21"
## [4425] "Ube2v1" "Aqp12" "Foxa1" "Sec23a"
## [4429] "Trappc6b" "Rpl7a-ps1" "Klhl28" "Fkbp3"
## [4433] "Mis18bp1" "Rpl10l" "Mdga2" "Dnaaf2"
## [4437] "Sned1" "Nemf" "Gm9887" "Vcpkmt"
## [4441] "Sos2" "L2hgdh" "Cdkl1" "Mir681"
## [4445] "Map4k5" "Gm23579" "Nin" "Ppp1r7"
## [4449] "Pygl" "Gpr135" "Ccdc175" "Rtn1"
## [4453] "Dhrs7" "4930447C04Rik" "Six1" "Six4"
## [4457] "D830013O20Rik" "Tmem30b" "Ano7" "Ppp2r5e"
## [4461] "Wdr89" "Gm7862" "Tex21" "Zbtb25"
## [4465] "Sptb" "Gm4864" "Atp6v1d" "Pigh"
## [4469] "Vti1b" "Farp2" "Zfyve26" "Gm8275"
## [4473] "Zfp36l1" "Actn1" "Dcaf5" "Adam4"
## [4477] "Adam21" "Med6" "Dpf3" "Zfyve1"
## [4481] "Bok" "Heatr4" "Gm26571" "Gm8385"
## [4485] "Pnma1" "Gm5436" "Entpd5" "Aldh6a1"
## [4489] "Syndig1l" "Prox2" "Rps6kl1" "Gm10550"
## [4493] "Mlh3" "Acyp1" "Erg28" "Tgfb3"
## [4497] "Irf2bpl" "Zdhhc22" "Tmed8" "Noxred1"
## [4501] "Vipas39" "Ism2" "Atg4b" "Sptlc2"
## [4505] "Alkbh1" "Cep128" "Gtf2a1" "Sel1l"
## [4509] "Lysmd1" "Gm4808" "1700019M22Rik" "Kcnk10"
## [4513] "Ptpn21" "Ing5" "Eml5" "Foxn3"
## [4517] "Efcab11" "Nrde2" "Ttc7b" "Gpr68"
## [4521] "Ccdc88c" "Ppp4r3a" "Tc2n" "Fbln5"
## [4525] "D2hgdh" "Ndufb1" "Lgmn" "Itpk1"
## [4529] "Prima1" "Asb2" "Ifi27l2b" "Serpina3c"
## [4533] "Gsc" "Dicer1" "Syne3" "Gbf1"
## [4537] "Fam174a" "Atg2b" "Bcl11b" "Setd3"
## [4541] "Degs2" "Mok" "Ankrd9" "Cdc42bpb"
## [4545] "Gm10425" "Gm266" "Ckb" "Gin1"
## [4549] "Bag5" "Ppp1r13b" "Atp5mj" "Tmem179"
## [4553] "Akt1" "Ahnak2" "Cdca4" "Gpr132"
## [4557] "Brf1" "Ighv5-7" "Slco6d1" "Igh-VX24"
## [4561] "V165-D-J-C mu" "Ighv1-72" "Gm9238" "Ighv1-83"
## [4565] "Ighv1-84" "Gm9260" "Dync2i1" "Dnah11"
## [4569] "Sp4" "Cntnap5b" "Gm54747" "Gm8598"
## [4573] "Speer6-ps1" "Gdi2" "Calm4" "Klf6"
## [4577] "Pitrm1" "Gm5191" "Idi1" "Dip2c"
## [4581] "Relch" "Heatr1" "Nid1" "Lyst"
## [4585] "Gng4" "B3galnt2" "Arid4b" "Psma2"
## [4589] "AW209491" "Gm25020" "Mplkip" "Tnfrsf11a"
## [4593] "Gpank1" "Yae1d1" "Vps41" "Amph"
## [4597] "Elmo1" "Gm7614" "Gm54437" "Gpx6"
## [4601] "Zscan12" "Isca1" "Zcchc2" "H2bc14"
## [4605] "H2bc22" "Zfp184" "H4c8" "H3c4"
## [4609] "H4c4" "H2bc4" "H1f2" "H2bc3"
## [4613] "H1f1" "Gm6651" "Trim38" "H2ac1"
## [4617] "BC005537" "Tdp2" "D130043K22Rik" "Dcdc2a"
## [4621] "Prl2c1" "Gm11360" "Agtr1a" "Dusp22"
## [4625] "Nifk" "Gm5447" "Foxq1" "Serpinb6b"
## [4629] "Ripk1" "Fam50b" "Prpf4b" "Gm22126"
## [4633] "Ppp1r3g" "Ly86" "Rreb1" "Tfcp2l1"
## [4637] "Riok1" "Snrnp48" "Pak1ip1" "Tmem14c"
## [4641] "Phactr1" "Nol7" "Rnf182" "Cd83"
## [4645] "Mylip" "Rbm24" "Gm42572" "Gm8321"
## [4649] "Cap2" "Rnf144b" "Id4" "Barx1"
## [4653] "Fam120aos" "Ninj1" "Ippk" "Tes3-ps"
## [4657] "Ogn" "Iars1" "Tmem185b" "Fbxw17"
## [4661] "S1pr3" "Cks2" "Gm22806" "Secisbp2"
## [4665] "Gadd45g" "Sfxn1" "Hrh2" "Cplx2"
## [4669] "Simc1" "3110009E18Rik" "Higd2a" "Faf2"
## [4673] "Eif4e1b" "Unc5a" "Zfp346" "Fgfr4"
## [4677] "Slc34a1" "BC038268" "Grk6" "Prr7"
## [4681] "C1ql2" "Tmed9" "B4galt7" "Caml"
## [4685] "Ddx46" "Txndc15" "Pcbd2" "Tgfbi"
## [4689] "Smad5" "Idnk" "Rmi1" "Ccdc93"
## [4693] "Naa35" "Dapk1" "Carnmt1" "Gm3338"
## [4697] "Me1" "Aopep" "Ercc6l2" "Habp4"
## [4701] "Cdk20" "Gm4810" "Slc35f5" "Spata31"
## [4705] "Spata31d1c" "Zfp369" "Zfp1000" "Cbx3"
## [4709] "Zfp997" "Ramacl" "Zfp759" "Rsl1"
## [4713] "Zfp273" "Gpr39" "Krbox5" "BC048507"
## [4717] "Fastkd3" "Gm4812" "Irx2" "Mrpl36"
## [4721] "Lpcat1" "Slc12a7" "Brd9" "Zdhhc11"
## [4725] "Gm23734" "Ccdc127" "Erap1" "Hnrnpa1l2-ps"
## [4729] "Pcsk1" "Gm19095" "Spata9" "Skic3"
## [4733] "2210408I21Rik" "Arb2a" "Gm8371" "Ccnt2"
## [4737] "Lysmd3" "Mblac2" "Cetn3" "Mef2c"
## [4741] "Ndufc1" "Gm5452" "Tmem161b" "Ccnh"
## [4745] "Gm8526" "Gm5667" "Ubxn4" "Tmem167"
## [4749] "Ssbp2" "Acot12" "Dhfr" "Serinc5"
## [4753] "Mtx3" "Homer1" "Arsb" "Tbca"
## [4757] "Otp" "Dcdc2b" "Derl1" "Thsd7b"
## [4761] "Wdr41" "Zbed3" "Poc5" "Gcnt4"
## [4765] "Fam169a" "Enc1" "Ankra2" "Gm9828"
## [4769] "Gm4815" "Zfp366" "Yod1" "Mrps27"
## [4773] "Ak6" "4932411K12Rik" "Cd180" "Sgtb"
## [4777] "Trim23" "Cenpk" "Srek1ip1" "Gm4938"
## [4781] "Nt5el" "Fcmr" "Dimt1" "Smim15"
## [4785] "Gm41056" "Rps3a3" "Actbl2" "Mier3"
## [4789] "Il6st" "Slc38a9" "Dhx29" "Ccno"
## [4793] "Slc41a1" "Mcidas" "Cdc20b" "Mir449c"
## [4797] "Mir449a" "Arl15" "4930544M13Rik" "Mocs2"
## [4801] "Gm10734" "Gm29767" "Emb" "Nucks1"
## [4805] "Gm9633" "B430218F22Rik" "4833420G17Rik" "Tmem267"
## [4809] "Calml3" "Net1" "Akr1e1" "Pfkp"
## [4813] "Gm10357" "Wdr37" "Slc45a3" "Zmynd11"
## [4817] "Gm16419" "Actn2" "Gpr137b" "Hnrnpf"
## [4821] "Tbce" "Ggps1" "Hecw1" "Mrpl32"
## [4825] "Sugct" "Elk4" "Cdk13" "Rala"
## [4829] "Stard3nl" "Epdr1" "Pgbd1" "Zscan26"
## [4833] "Nkapl" "Cox5b" "Zfp389" "H2ac15"
## [4837] "Lemd1" "H1f5" "H4c9" "Vmn1r190-ps"
## [4841] "Zfp322a" "Abt1" "H2bc9" "H4c6"
## [4845] "H2ac8" "H4c3" "4930558J22Rik" "Gm7241"
## [4849] "Gm11337" "Slc17a4" "H2bc1" "Scgn"
## [4853] "Carmil1" "Gmnn" "Acot13" "Aldh5a1"
## [4857] "Mrs2" "Gm11349" "Klhdc8a" "Sox4"
## [4861] "E2f3" "Uqcrfs1" "Hus1b" "1700018A04Rik"
## [4865] "Gmds" "D930007J09Rik" "Serpinb9c" "Serpinb6a"
## [4869] "Tubb2a" "Gm22079" "Nuak2" "Pxdc1"
## [4873] "Fam217a" "Eci2" "Rpp40" "Nrn1"
## [4877] "F13a1" "Ssr1" "Txndc5" "Bloc1s5"
## [4881] "Eef1e1" "Dstyk" "Slc35b3" "Rps17-ps1"
## [4885] "Nedd9" "Adtrp" "Tbc1d7" "Dtnbp1"
## [4889] "Atxn1" "Kif13a" "Nhlrc1" "Tpmt"
## [4893] "Rbbp5" "Dek" "Zfp169" "Phf2"
## [4897] "Susd3" "Cenpp" "Shc3" "Sema4d"
## [4901] "Auh" "Ror2" "Gm38564" "Tmem81"
## [4905] "Drd1" "4833439L19Rik" "Nop16" "Cltb"
## [4909] "Rnf44" "Sncb" "Uimc1" "Rab24"
## [4913] "Mxd3" "Lman2" "Gm10538" "Pfn3"
## [4917] "F12" "Dbn1" "Ddx41" "Fam193b"
## [4921] "4930451E10Rik" "Pitx1" "Spock1" "Klhl3"
## [4925] "Hnrnpa0" "Lrrn2" "Gkap1" "Kif27"
## [4929] "Qng1" "Mir7-1" "4921517D22Rik" "Spata31d1a"
## [4933] "Spata31d1d" "Zfp935" "Zfp1008" "Gm7045"
## [4937] "Plekha6" "Platr25" "Fbp2" "Fancc"
## [4941] "Ptch1" "Rpl10a" "Hsd17b3" "Prxl2c"
## [4945] "Ctsl" "Cntnap3" "Prss47" "Ren1"
## [4949] "Mfsd14b" "Zfp640" "Gm33043" "BC049692"
## [4953] "Mterf3" "Rslcan18" "Zfp458" "Zfp457"
## [4957] "Zfp595" "Zfp953" "Gm10537" "Zfp456"
## [4961] "Zfp874a" "Zfp58" "Zfp87" "Zfp748"
## [4965] "Zfp729b" "Zfp729a" "Zfp738" "Tent4a"
## [4969] "Srd5a1" "Chit1" "Ice1" "Irx1"
## [4973] "Slc6a18" "Nkd2" "Trip13" "Exoc3"
## [4977] "Pdcd6" "Zfp72" "Zfp825" "Cast"
## [4981] "Naxe" "Chi3l1" "Gm8278" "Gm3926"
## [4985] "Rhobtb3" "Arsk" "Fam81b" "Slf1"
## [4989] "Gm5042" "Gm8345" "Adgrv1" "Polr3g"
## [4993] "Mybph" "Gm5666" "Gm12338" "Gm8546"
## [4997] "Xrcc4" "Atp6ap1l" "Atg10" "4833422C13Rik"
## [5001] "Zcchc9" "Ckmt2" "Msh3" "Mgat4f"
## [5005] "Zfyve16" "Thbs4" "Tent2" "Jmy"
## [5009] "Bhmt" "Bhmt2" "Scamp1" "Pde8b"
## [5013] "Aggf1" "Crhbp" "Cyb5r1" "F2r"
## [5017] "Iqgap2" "Sv2c" "Polk" "Hexb"
## [5021] "Btf3" "Sec61b" "Tmem171" "Fcho2"
## [5025] "Tnpo1" "Adipor1" "H2bl1" "Ptcd2"
## [5029] "Map1b" "Cartpt" "BC001981" "Gm54974"
## [5033] "Gtf2h2" "Marveld2" "Rad17" "Cdk7"
## [5037] "Ube2t" "Mrps36" "Cenph" "Slc30a5"
## [5041] "Gm6114" "Pik3r1" "Srek1" "Nln"
## [5045] "Trappc13" "Ppwd1" "Cwc27" "Gm10535"
## [5049] "Rgs7bp" "Ipo11" "Kif2a" "Ndufaf2"
## [5053] "Gm30747" "Gemin8" "Gapt" "Gpbp1"
## [5057] "Map3k1" "Gpx8" "Arl8a" "Gm41069"
## [5061] "Snx18" "Ndufs4" "Fst" "Itga2"
## [5065] "Parp8" "Gm17509" "Gm5200" "Mrps30"
## [5069] "3110070M22Rik" "Csrp1" "Zfp131" "Nim1k"
## [5073] "Gm3500" "Gm3095" "Slbp" "Flnb"
## [5077] "Abhd6" "Rpp14" "Pxk" "Kctd6"
## [5081] "Phlda3" "Ptprg" "Cep15" "Synpr"
## [5085] "Sntn" "Slc4a7" "Nek10" "Ngly1"
## [5089] "Top2b" "Gm7084" "Nkiras1" "Cox18"
## [5093] "Tnnt2" "Gm12202" "Gm8582" "Nid2"
## [5097] "Fam149b" "1810062O18Rik" "Sec24c" "Fut11"
## [5101] "Chchd1" "Vcl" "Adk" "Tmem9"
## [5105] "Lrmda" "Cnot1" "E330034G19Rik" "Gm18276"
## [5109] "Zmiz1" "Ppif" "Anxa11" "4933413J09Rik"
## [5113] "Gm24031" "9930004E17Rik" "Kif21b" "Dnah12"
## [5117] "Asb14" "Il17rd" "Arhgef3" "Erc2"
## [5121] "Lrtm1" "Actr8" "Chdh" "Dcp1a"
## [5125] "Tkt" "Kif14" "Rft1" "Sfmbt1"
## [5129] "Stimate" "Pbrm1" "Nt5dc2" "Tnnc1"
## [5133] "Sema3g" "Bap1" "Eaf1" "Galnt15"
## [5137] "Zfp281" "Oxnad1" "Parg" "Ogdhl"
## [5141] "Drgx" "Vstm4" "Lrrc18" "Gm6340"
## [5145] "Frmpd2" "Gdf10" "Gm5460" "Dennd1b"
## [5149] "Antxrl" "Syt15" "Glud1" "Grid1"
## [5153] "Mir346" "4930474N05Rik" "Gm5203" "Eif1-ps1"
## [5157] "Gm2791" "Dydc1" "Zbtb41" "Sftpa1"
## [5161] "Ear2" "BC061237" "Bnip3" "Psmc6"
## [5165] "Cdkn3" "Cgrrf1" "Socs4" "Mapk1ip1l"
## [5169] "Lgals3" "Aspm" "Fbxo34" "Ktn1"
## [5173] "Peli2" "Tmem260" "Ap5m1" "Naa30"
## [5177] "Or11g27" "Parp2" "Pnp" "Apex1"
## [5181] "Uchl5" "Rnase4" "Rnase6" "Rnase2b"
## [5185] "Gm7247" "Gm5622" "AY358078" "Ear7"
## [5189] "Mettl17" "Slc39a2" "Tppp2" "Gm5263"
## [5193] "Arhgef40" "Rpgrip1" "Tox4" "Or4e2"
## [5197] "Trav2" "Trav3-1" "Trav8d-1" "Trav13d-4"
## [5201] "Trav4d-4" "Trav6d-6" "Ppm1a" "Brinp3"
## [5205] "Trav4-2" "Trav8-1" "Trav15-2-dv6-2" "Trav13-5"
## [5209] "Trdv2-1" "Traj57" "Abhd4" "Oxa1l"
## [5213] "Mmp14" "Lrp10" "Tpr" "Rem2"
## [5217] "Gm42368" "Psmb11" "4930579G18Rik" "1700123O20Rik"
## [5221] "Rnf212b" "Bcl2l2" "Cmtm5" "Mhrt"
## [5225] "Ngdn" "Niban1" "Gm10364" "Carmil3"
## [5229] "Cpne6" "Dcaf11" "Fitm1" "Psme1"
## [5233] "Rnf31" "Ltb4r2" "Ltb4r1" "Khnyn"
## [5237] "Edem3" "Atp12a" "2410022M11Rik" "Ift88"
## [5241] "Il17d" "Sap18" "Fgf9" "Rpl13"
## [5245] "Rcbtb1" "Cab39l" "Shisa2" "Apobec4"
## [5249] "Gm6066" "Arl11" "Trim13" "Rnaseh2b"
## [5253] "Fam124a" "Serpine3" "Wdfy2" "Ctsb"
## [5257] "Fam167a" "Xkr6" "Arpc5" "Mir598"
## [5261] "Pinx1" "Sox7" "Prss51" "Prss52"
## [5265] "Kif13b" "Zfp395" "Nuggc" "Scara5"
## [5269] "Pbk" "Nmnat2" "Ccdc25" "Clu"
## [5273] "Trim35" "Pnma2" "Gm9570" "Kctd9"
## [5277] "Gnrh1" "Nkx2-6" "Tnfrsf10b" "Egr3"
## [5281] "Shcbp1l" "Bin3" "1700031C06Rik" "Gm9174"
## [5285] "Mir320" "Reep4" "Hr" "Nudt18"
## [5289] "Dok2" "Gfra2" "Rcbtb2" "Rgs16"
## [5293] "Lpar6" "Med4" "Esd" "Gm10847"
## [5297] "Zc3h13" "Siah3" "Erich6b" "Snora31"
## [5301] "Nufip1" "4930431P22Rik" "Stx6" "Ccdc122"
## [5305] "Enox1" "Epsti1" "Gm4821" "Mtrf1"
## [5309] "Kbtbd7" "Elf1" "Sugt1" "Pcdh17"
## [5313] "Gm9264" "Atg5" "Acbd6" "Tdrd3"
## [5317] "Ccdc202" "Snora30" "Pibf1" "Klf5"
## [5321] "4930517O19Rik" "Lmo7" "Cln5" "Slain1"
## [5325] "Ndfip2" "Tor1aip2" "Trim52" "Frg2f4"
## [5329] "Slitrk5" "Mir17hg" "Gpc6" "Dnajc3"
## [5333] "Cldn10" "Hs6st3" "Rap2a" "Gm25781"
## [5337] "Nphs2" "Timm8a2" "Tm9sf2" "Clybl"
## [5341] "Gm10837" "Pcca" "4930594M22Rik" "Itgbl1"
## [5345] "4930469B13Rik" "Fam107a" "Fam3d" "Abl2"
## [5349] "Cfap20dc" "Gm43041" "Ptma" "Fhit"
## [5353] "Rpl19" "Thoc7" "Psmd6" "Gm8483"
## [5357] "Oxsm" "Rarb" "Pclaf" "Gm55487"
## [5361] "Nr1d2" "Ube2e2" "Gng2" "Saysd1"
## [5365] "Kcnk5" "Ecd" "Mrps16" "Cfap70"
## [5369] "Mss51" "Gm34423" "Ppp3cb" "Usp54"
## [5373] "Synpo2l" "Ndst2" "Camk2g" "Gm6128"
## [5377] "Ap3m1" "Dusp29" "Comtd1" "Kcnma1"
## [5381] "Astn1" "Dlg5" "Gm52995" "Polr3a"
## [5385] "4930542C16Rik" "Ppifos" "1700054O19Rik" "Zcchc24"
## [5389] "Plac9" "Slmap" "Arf4os" "Gm31256"
## [5393] "Pde12" "Ccdc66" "Il17rb" "Cacna1d"
## [5397] "Uqcc5" "Sh3bp5" "Hacl1" "Slc18a3"
## [5401] "3425401B19Rik" "Wdfy4" "Gm10530" "Mapk8"
## [5405] "Gprin2" "Shld2" "Fam25a" "Sncg"
## [5409] "Bmpr1a" "9230112D13Rik" "Ldb3" "Opn4"
## [5413] "4930596D02Rik" "4930523C07Rik" "Gm7853" "Ccser2"
## [5417] "Rgr" "Gpr15lg" "Ghitm" "Tspan14"
## [5421] "Prxl2a" "Dydc2" "Ero1a" "Fermt2"
## [5425] "Rragc" "Mrps14" "Cnih1" "Gmfb"
## [5429] "Gm10371" "Wdhd1" "Dlgap5" "Atg14"
## [5433] "Map1lc3b" "Exoc5" "Ccdc198" "Gm22116"
## [5437] "Rpl23a" "Or4n4" "Or4n4b" "Or4m1"
## [5441] "Or4q3" "Ttc5" "Ccnb1ip1" "Rpph1"
## [5445] "Tep1" "Osgep" "Pip4p1" "Rc3h1"
## [5449] "Rnase11" "Or6s1" "Rnase1" "Gm5800"
## [5453] "Ndrg2" "Zfp219" "Hnrnpc" "Chd8"
## [5457] "Snord8" "Rab2b" "Serpinc1" "Mettl3"
## [5461] "Or10g3" "Or10g1" "Nrbf2" "A630038E17Rik"
## [5465] "Dad1" "Prmt5" "Haus4" "Ajuba"
## [5469] "Psmb5" "Gas5" "Cdh24" "Acin1"
## [5473] "Cebpe" "Slc7a8" "Homez" "Ppp1r3e"
## [5477] "Slc22a17" "Efs" "Myh7" "Zfhx2"
## [5481] "Cenpl" "Jph4" "Gm10876" "A730061H03Rik"
## [5485] "Psme2" "Tm9sf1" "Mdp1" "Tinf2"
## [5489] "Cideb" "Sdr39u1" "Gm5801" "Ankrd45"
## [5493] "Gzmn" "Cpap" "Zmym5" "Gja3"
## [5497] "Gjb2" "Cryl1" "Ska3" "Zdhhc20"
## [5501] "Micu2" "1700129C05Rik" "SLC9C2" "Gm5142"
## [5505] "Phf11c" "Setdb2" "Cdadc1" "Gm47810"
## [5509] "Mipepos" "Tnfrsf19" "Ebpl" "Kpna3"
## [5513] "Spryd7" "Gm10176" "Mir15a" "Defb30"
## [5517] "Fdft1" "Gata4" "Mtmr9" "4930578I06Rik"
## [5521] "Hmbox1" "Extl3" "Fzd3" "Pnoc"
## [5525] "Vamp4" "Elp3" "Esco2" "Ptk2b"
## [5529] "Dpysl2" "Ppp2r2a" "Dock5" "Slc25a37"
## [5533] "R3hcc1" "Chmp7" "Gm17740" "Gm29093"
## [5537] "Myoc" "Rhobtb2" "Ccar2" "Pdlim2"
## [5541] "Sorbs3" "Ppp3cc" "Slc39a14" "Polr3d"
## [5545] "Bmp1" "Fhip2b" "Dmtn" "Kifap3"
## [5549] "Fgf17" "Npm2" "Rb1" "Lrch1"
## [5553] "Lrrc63" "Cby2" "Gm25517" "Gpalpp1"
## [5557] "Serp2" "Fkbp1a-ps1" "Scyl3" "Lacc1"
## [5561] "Gm1587" "Dnajc15" "Tnfsf11" "Akap11"
## [5565] "Naa16" "Wbp4" "Cnmd" "Gm10845"
## [5569] "Gm33121" "Mettl18" "Rps3a1" "Pcdh20"
## [5573] "Gm7272" "Gm7232" "Pcdh9" "Dach1"
## [5577] "Mzt1" "Klf12" "Gm9302" "Tbc1d4"
## [5581] "Sele" "Commd6" "Gm9922" "Gm5854"
## [5585] "Fbxl3" "Mycbp2" "Obi1" "Rpl27a-ps2"
## [5589] "Slitrk1" "Dct" "Tgds" "F5"
## [5593] "Sox21" "Abcc4" "Dzip1" "Stk24"
## [5597] "Dock9" "Gm5089" "Gm9399" "Tmtc4"
## [5601] "Fgf14" "Selenop" "Slc19a2" "Oxct1"
## [5605] "Prkaa1" "Ttc33" "Dab2" "C9"
## [5609] "Fyb1" "Rictor" "Lifr" "Gdnf"
## [5613] "Nup155" "Ccdc181" "Cplane1" "Capsl"
## [5617] "Prlr" "Rad1" "C1qtnf3" "Amacr"
## [5621] "Zfr" "Golph3" "Gm19840" "Cdh18"
## [5625] "Nme7" "Myo10" "Retreg1" "Zfp622"
## [5629] "Marchf11" "Ank" "Dnah5" "Ctnnd2"
## [5633] "Cmbl" "Atpsckmt" "Sema5a" "Gpr161"
## [5637] "Sdc2" "Cpq" "Mtdh" "Laptm4b"
## [5641] "Erich5" "Osr2" "Gm18994" "Gm22979"
## [5645] "Polr2k" "Spag1" "Mir8101" "Mpc2"
## [5649] "Grhl2" "Cthrc1" "Dcaf13" "Zfpm2"
## [5653] "Emc2" "Gm2140" "Eny2" "Pkhd1l1"
## [5657] "Ebag9" "A930017M01Rik" "Adcy10" "4930548G14Rik"
## [5661] "Aard" "Med30" "Gm7489" "Colec10"
## [5665] "Ccn3" "Deptor" "Col14a1" "Mtbp"
## [5669] "Zhx2" "Creg1" "Tbc1d31" "Fam83a"
## [5673] "Ntaq1" "Trmt12" "Ndufb9" "Gm7691"
## [5677] "Sqle" "Nsmce2" "Tsg101" "Gsdmcl-ps"
## [5681] "Cd247" "Efr3a" "Phf20l1" "Ccn4"
## [5685] "Gm41341" "Khdrbs3" "Chrac1" "Ptp4a3"
## [5689] "Gm22106" "Adgrb1" "4933427E11Rik" "Gpa33"
## [5693] "Psca" "Them6" "Gml2" "Ly6e"
## [5697] "Ly6f" "Gpihbp1" "Zfp41" "Gm38506"
## [5701] "Rhpn1" "Tigd5" "Ildr2" "Zfp707"
## [5705] "Mapk15" "Spatc1" "Smpd5" "Exosc4"
## [5709] "Gpaa1" "Cyc1" "Maf1" "Wdr97"
## [5713] "Hgh1" "Aldh9a1" "Mroh1" "Hsf1"
## [5717] "Adck5" "Kifc2" "Ppp1r16a" "Lrrc14"
## [5721] "Commd5" "Rpl8" "1110038F14Rik" "Apol10a"
## [5725] "Lmx1a" "Csf2rb" "Kctd17" "1700041B01Rik"
## [5729] "Gga1" "Sh3bp1" "Lgals1" "Triobp"
## [5733] "H1f0" "Galr3" "Eif3l" "Rgs5"
## [5737] "Pick1" "Maff" "Cby1" "Tomm22"
## [5741] "Gtpbp1" "Gm55311" "Apobec3" "Syngr1"
## [5745] "Mgat3" "Mief1" "4930500M09Rik" "Cacna1i"
## [5749] "Adsl" "4930483J18Rik" "Mchr1" "Xpnpep3"
## [5753] "Rbx1" "Ep300" "Zc3h7b" "Aco2"
## [5757] "Csdc2" "Ddb1" "Spata46" "Gm5805"
## [5761] "Ndufb11b" "Xrcc6" "4930407I10Rik" "Mei1"
## [5765] "Ccdc134" "Smim45" "Smdt1" "Gm54394"
## [5769] "Cyp2d9" "Gm7299" "Rnu12" "Bik"
## [5773] "Tspo" "Mpped1" "Pnpla3" "Samm50"
## [5777] "Parvb" "Prr5" "Arhgap8" "Nup50"
## [5781] "Olfml2b" "Upk3a" "Fam118a" "Ribc2"
## [5785] "Ppara" "Ttc38" "Gramd4" "Tbc1d22a"
## [5789] "Tafa5" "Creld2" "Gm33049" "Gm9929"
## [5793] "Mov10l1" "Panx2" "Trabd" "Selenoo"
## [5797] "Ppp6r2" "Ncaph2" "C730034F03Rik" "Mapk8ip2"
## [5801] "Acr" "Gm3861" "Gm26620" "Lrrk2"
## [5805] "Irak4" "Tmem117" "Ano6" "Pced1b"
## [5809] "Slc48a1" "Pfkm" "Ccdc184" "1700031M16Rik"
## [5813] "Or8s10" "Cfap126" "Or5bs2" "Or11m3"
## [5817] "9330020H09Rik" "Spmip11" "Cacnb3" "Ccdc65"
## [5821] "B130046B21Rik" "Rpl36" "Troap" "Prpf40b"
## [5825] "Mpz" "Tmbim6" "Aqp2" "Aqp5"
## [5829] "Asic1" "Smarcd1" "Cox14" "Larp4"
## [5833] "Tmprss12" "Tmt1a" "Letmd1" "Apoa2"
## [5837] "Dazap2" "Scn8a" "Eif4b" "Igfbp6"
## [5841] "Gm9918" "Mfsd5" "Espl1" "Pfdn5"
## [5845] "Myg1" "Map3k12" "B4galt3" "Tarbp2"
## [5849] "Hoxc9" "Hoxc8" "Mir615" "Gm10830"
## [5853] "Copz1" "Nckap1l" "Gm7962" "Ghr"
## [5857] "Gm4823" "Nectin4" "C7" "Card6"
## [5861] "Atp5pd" "Osmr" "Egflam" "Slc1a3"
## [5865] "Gm5210" "Spef2" "Dnajc21" "Brix1"
## [5869] "Gm47260" "1700037C18Rik" "Arhgap30" "Ttc23l"
## [5873] "Gm8174" "Rai14" "Tars1" "Npr3"
## [5877] "Pdzd2" "6030458C11Rik" "Cdh6" "Gm8328"
## [5881] "Gm8341" "Usf1" "Acot10" "Basp1"
## [5885] "Fbxl7" "Otulin" "Trio" "Gm26163"
## [5889] "Ankrd33b" "Ropn1l" "Ube2v2" "Marchf6"
## [5893] "F11r" "Cct5" "Rpl30" "Rida"
## [5897] "Stk3" "Cox6c" "Fbxo43" "Ywhaz"
## [5901] "Zfp706" "Gm9509" "Gm8664" "Alyref2"
## [5905] "Ncald" "Gm8705" "Klf10" "G930009F23Rik"
## [5909] "Slc25a32" "Eif3e" "Nudcd1" "Sybu"
## [5913] "Gm5471" "Gm5472" "Cd48" "Csmd3"
## [5917] "Eif3h" "Ext1" "Samd12" "Tnfrsf11b"
## [5921] "Enpp2" "Taf2" "Dscc1" "Mrpl13"
## [5925] "Sntb1" "Tma7" "9130401M01Rik" "Tmem65"
## [5929] "Ube2d4" "Tatdn1" "Mtss1" "4933412E24Rik"
## [5933] "Gm24696" "Macroh2a3" "Gm25702" "Gm4942"
## [5937] "Pex19" "Gsdmc2" "Cyrib" "Asap1"
## [5941] "Oc90" "Hhla1" "Kcnq3" "Ndrg1"
## [5945] "Zfat" "Mir30d" "Gm7859" "Pigm"
## [5949] "Fam135b" "Trappc9" "Ago2" "Gpr20"
## [5953] "Mroh5" "Sf3b4" "Arc" "Jrk"
## [5957] "Slurp1" "Slurp2" "Slamf9" "Ly6d"
## [5961] "Ly6g6g" "Ly6k" "Gml" "Cyp11b1"
## [5965] "Cyp11b2" "Ly6m" "Ly6a" "Top1mt"
## [5969] "Mafa" "Igsf9" "Naprt" "Eef1d"
## [5973] "Gfus" "Ccdc166" "Eppk1" "Plec"
## [5977] "Parp10" "Mirt2" "Oplah" "Tssk5"
## [5981] "Snapin" "Tagln2" "Rpl29" "Tmem249"
## [5985] "Fbxl6" "Cpsf1" "Slc39a4" "Tonsl"
## [5989] "Lrrc24" "Arhgap39" "Zfp251" "Mb"
## [5993] "Cfap45" "Apol8" "Myh9" "Txn2"
## [5997] "Eif3d" "Cacng2" "Ift27" "Csf2rb2"
## [6001] "Cimip4" "Tst" "Tmprss6" "Vsig8"
## [6005] "C1qtnf6" "Elfn2" "Card10" "Ankrd54"
## [6009] "Sox10" "Slc16a8" "Baiap2l2" "Pla2g6"
## [6013] "Tmem184b" "Csnk1e" "Crp" "Ddx17"
## [6017] "Dmc1" "Josd1" "Sun2" "Dnal4"
## [6021] "D730005E14Rik" "Cbx7" "Pdgfb" "Enthd1"
## [6025] "Mrtfa" "Or10j5" "Slc25a17" "St13"
## [6029] "Dnajb7" "Tob2" "Phf5a" "Polr3h"
## [6033] "Pmm1" "Snu13" "Tnfrsf13c" "Cenpm"
## [6037] "Or6n2" "Naga" "Ndufa6" "Cyp2d22"
## [6041] "Cyp2d10" "Cyp2d37-ps" "Cyp2d40" "Cyp2d41-ps"
## [6045] "Cyp2d26" "Tbrg3" "Rrp7a" "Spta1"
## [6049] "Cyb5r3" "Vkorc1l1" "Ttll1" "Mcat"
## [6053] "Ttll12" "Scube1" "Efcab6" "Sult4a1"
## [6057] "Gm5214" "Phf21b" "Or6p1" "5031439G07Rik"
## [6061] "Smc1b" "Pkdrej" "Cerk" "Alg12"
## [6065] "Mlc1" "Hdac10" "Plxnb2" "Dennd6b"
## [6069] "Sbf1" "Exo1" "Lmf2" "Cimap1b"
## [6073] "Arsa" "Rabl2" "Cpne8" "Kif21a"
## [6077] "Abcd2" "Slc2a13" "Gxylt1" "Zcrb1"
## [6081] "Sdccag8" "Prickle1" "Adamts20" "Pus7l"
## [6085] "Twf1" "Nell2" "Scaf11" "Slc38a1"
## [6089] "Slc38a2" "Gm8888" "Amigo2" "Atox1"
## [6093] "Spmip3" "Hdac7" "Vdr" "Col2a1"
## [6097] "Asb8" "Zfp641" "Or8s5" "Kansl2"
## [6101] "Ccnt1" "Ddx23" "Arf3" "Catspere2"
## [6105] "Wnt10b" "Kmt2d" "Lmbr1l" "Tuba1a"
## [6109] "C1ql4" "Mcrs1" "Fam186b" "Gm22951"
## [6113] "Nckap5l" "Racgap1" "Desi2" "Lima1"
## [6117] "Fam186a" "2310068J16Rik" "Slc11a2" "Csrnp2"
## [6121] "Tfcp2" "Smagp" "Bin2" "Krt87"
## [6125] "Krt82" "Cox20" "Krt75" "Gm5414"
## [6129] "Krt6b" "Krt5" "Krt73" "Krt1"
## [6133] "Krt77" "Krt79" "Krt8" "Csad"
## [6137] "Gm24405" "Npff" "Atf7" "Mir688"
## [6141] "Calcoco1" "Cbx5" "Zfp385a" "Gtsf1"
## [6145] "Gtsf2" "Gm9108" "Or1f19" "Cnst"
## [6149] "Zfp263" "Gm54882" "Zfp174" "Cluap1"
## [6153] "Vasn" "Hmox2" "4930562C15Rik" "Mgrn1"
## [6157] "Dnaaf8" "Ubn1" "Gm10518" "Sec14l5"
## [6161] "Mettl22" "Pmm2" "Gm7572" "Rpl39l"
## [6165] "Atf7ip2" "Nubp1" "Clec16a" "Snn"
## [6169] "Snx29" "Cdc42bpa" "Gm9961" "Shisa9"
## [6173] "Ercc4" "Mrtfb" "Mir365-1" "Bfar"
## [6177] "Ntan1" "Mpv17l" "Bmerb1" "Mir484"
## [6181] "Itpkb" "Nde1" "Gm1758" "A630010A05Rik"
## [6185] "Snai2" "Clxn" "Prkdc" "Pkp2"
## [6189] "Yars2" "Ppm1f" "Gm6438" "Parp1"
## [6193] "Ydjc" "Hic2" "Serpind1" "Snap29"
## [6197] "Aifm3" "Lztr1" "P2rx6" "Smpd4"
## [6201] "Ccdc74a" "Scarf2" "Snrnp27" "Lin9"
## [6205] "Fam246a" "Tssk1" "Tssk2" "Vpreb1b"
## [6209] "Gm49580" "Dgcr6" "Rtn4r" "Trmt2a"
## [6213] "Gnb1l" "4930588K23Rik" "H3f3aos" "Gm10088"
## [6217] "Gm17799" "Yeats2" "Eif2b5" "Dvl3"
## [6221] "Ap2m1" "Abcf3" "Polr2h" "Chrd"
## [6225] "Gm9697" "Sde2" "Map3k13" "Ndufa11"
## [6229] "Gm26980" "Dnajb11" "Fetub" "St6gal1"
## [6233] "Rtp1" "Rtp4" "Lpp" "Mir28a"
## [6237] "Pycr2" "Trp63" "Ccdc50" "Hes1"
## [6241] "1700025H01Rik" "Bdh1" "Meltf" "Ncbp2"
## [6245] "Cep19" "Smco1" "Ubxn7" "Cnih4"
## [6249] "Dynlt2b" "Pcyt1a" "Zdhhc19" "Tfrc"
## [6253] "Tnk2" "Muc4" "Lmln" "Snx4"
## [6257] "Heg1" "Itgb5" "Srp9" "Ropn1"
## [6261] "Mylk" "Hacd2" "Kpna1" "Wdr5b"
## [6265] "Mix23" "Ildr1" "Iqcb1" "Golgb1"
## [6269] "Hcls1" "Trp53bp2" "Rabl3" "Fstl1"
## [6273] "Lrrc58" "Gpr156" "Cox17" "Popdc2"
## [6277] "Tmem39a" "Igsf11" "Zbtb20" "Ccdc191"
## [6281] "Capn8" "Naa50" "Usf3" "Spice1"
## [6285] "Nepro" "Ccdc80" "Atg3" "Gm5406"
## [6289] "Slc9c1" "Gm6912" "Gm7275" "Rab3gap2"
## [6293] "Gm17804" "Prdx1" "Morc1" "Myh15"
## [6297] "Ift57" "Cd47" "Gm8824" "1700116B05Rik"
## [6301] "Cblb" "Rpl24" "Mir194-1" "Zbtb11"
## [6305] "Senp7" "Abi3bp" "Tomm70a" "Filip1l"
## [6309] "Dcbld2" "Cpox" "Cldnd1" "Gabrr3"
## [6313] "Orai2" "Gm23645" "Bpnt1" "Riox2"
## [6317] "Sinhcaf" "Gm25986" "Pros1" "Vgll3"
## [6321] "4933411O13Rik" "Gbe1" "Robo1" "Rbm11"
## [6325] "Mir99ahg" "Eprs1" "Gm21816" "Mir99a"
## [6329] "Mirlet7c-1" "Cxadr" "Fkbp1a-ps3" "Jam2"
## [6333] "Gabpa" "Gm10791" "N6amt1" "Usp16"
## [6337] "Slc30a10" "Map3k7cl" "Bach1" "Krtap13-23"
## [6341] "krtap20-23" "Krtap20-20" "Gm2805" "Sod1"
## [6345] "Hunk" "1110008E08Rik" "Mrap" "Gm26169"
## [6349] "Eva1c" "Olig1" "Ifnar2" "Il10rb"
## [6353] "Ifnar1" "Ifngr2" "Gm10785" "Slc5a3"
## [6357] "Kcne2" "Smim11" "Gm3809" "Cbr1"
## [6361] "Dop1b" "Morc3" "Chaf1b" "Dyrk1a"
## [6365] "Ets2" "1700093J21Rik" "Get1" "Igsf5"
## [6369] "B230307C23Rik" "Ush2a" "Zfp597" "Crebbp"
## [6373] "Adcy9" "Srl" "Pam16" "Coro7"
## [6377] "Anks3" "Nagpa" "AU021092" "Gm55020"
## [6381] "Ptpn14" "Tmem114" "Tmem186" "Carhsp1"
## [6385] "Emp2" "Tvp23a" "Dexi" "Tnp2"
## [6389] "Prm3" "Prm1" "Litaf" "A230020J21Rik"
## [6393] "Zc3h7a" "Gm24145" "Rsl1d1" "Gspt1"
## [6397] "Cpped1" "Gm6332" "2310015D24Rik" "Parn"
## [6401] "Pla2g10" "Ifitm7" "Spata45" "Myh11"
## [6405] "Cep20" "Gm7731" "Mzt2" "Dnm1l"
## [6409] "Fgd4" "Or7a40" "4933404G15Rik" "Vpreb1a"
## [6413] "Gm9974" "Nsl1" "Ppil2" "Mir130b"
## [6417] "Thap7" "Med15" "Car15" "Ess2"
## [6421] "Gsc2" "Slc25a1" "Prodh" "4933432I09Rik"
## [6425] "Gm15573" "Batf3" "Ranbp1" "Dgcr8"
## [6429] "Mir185" "Comt" "Tbx1" "Cdc45"
## [6433] "Mrpl40" "Iglv1" "Map6d1" "Abcc5"
## [6437] "D730003I15Rik" "Gm15760" "Alg3" "Clcn2"
## [6441] "Rps10" "Magef1" "2510009E07Rik" "Tmem41a"
## [6445] "Tra2b" "Crygs" "Tbccd1" "Pacc1"
## [6449] "Rfc4" "BC106179" "Gm6640" "Sst"
## [6453] "P3h2" "Fgf12" "Mb21d2" "Lrrc15"
## [6457] "Tmem44" "Lsg1" "Nek2" "Ncbp2as2"
## [6461] "Pigx" "Iqcg" "Umps" "Sec22a"
## [6465] "Gm5963" "Fam162a" "Casr" "Eaf2"
## [6469] "Fbxo40" "Rd3" "Stxbp5l" "Pla1a"
## [6473] "Adprh" "Timmdc1" "Poglut1" "Arhgap31"
## [6477] "Gm15575" "Upk1b" "Tex55" "4932412D23Rik"
## [6481] "Gm10516" "Tigit" "Qtrt2" "Zdhhc23"
## [6485] "Atp6v1a" "Sidt1" "Gtpbp8" "Slc35a5"
## [6489] "Cd200" "Cd200l1" "Tagln3" "Kcnh1"
## [6493] "Abhd10" "Phldb2" "Plcxd2" "Cd96"
## [6497] "Dzip3" "Gm22576" "Gm5407" "Gm4802"
## [6501] "Ccdc54" "Psmc1" "Irf6" "Gm6767"
## [6505] "Nfkbiz" "Nxpe3" "Cep97" "Zbtb11os1"
## [6509] "Pcnp" "Trmt10c" "Adgrg7" "Tmem45a"
## [6513] "Tmem45a2" "A130010J15Rik" "Nit2" "Tbc1d23"
## [6517] "Tmem30c" "Cmss1" "St3gal6" "Ftdc2"
## [6521] "Gpr15" "Or5k1" "Or5ac20" "Arl6"
## [6525] "Plxna2" "Nsun3" "Arl13b" "Epha3"
## [6529] "Csnk2a2ip" "Zfp654" "Gm16385" "Htr1f"
## [6533] "Chmp2b" "Cadm2" "Speer2" "Tomm5"
## [6537] "Cd34" "Lipi" "Hspa13" "Nrip1"
## [6541] "Gm7334" "D16Ertd472e" "Rps19-ps12" "Gm54838"
## [6545] "Rpl21" "Gm6032" "Mrpl39" "A330023F24Rik"
## [6549] "Atp5pf" "App" "Cyyr1" "Adamts1"
## [6553] "Adamts5" "Ltn1" "Cct8" "Rpl31-ps4"
## [6557] "Krtap19-2" "Krtap19-4" "Xkr4" "Krtap19-9a"
## [6561] "Krtap16-3" "Gm41515" "Krtap6-5" "Krtap8-1"
## [6565] "Krtap11-1" "Tiam1" "Mis18a" "Cfap298"
## [6569] "Synj1" "Sox17" "Paxbp1" "Epcip"
## [6573] "H3f3a-ps2" "Gm9881" "Dnajc28" "Atp5po"
## [6577] "Fam243" "Rcan1" "Cldn14" "Hlcs"
## [6581] "Gm6085" "Pigp" "Kcnj6" "Psmg1"
## [6585] "Hmgn1" "Lca5l" "Itgb2l" "Fam3b"
## [6589] "Prdm15" "A630089N07Rik" "Scaf8" "Mrpl15"
## [6593] "Cldn20" "Arid1b" "Gtf2h5" "Tulp4"
## [6597] "Tmem181a" "Gm1604b" "Cep43" "Mpc1"
## [6601] "T2" "T" "Hmgb3" "Prkn"
## [6605] "Agpat4" "Gm6618" "Airn" "Snora20"
## [6609] "Gm10512" "Smok2a" "Smok2b" "Gm7168"
## [6613] "Smoc2" "4732440D04Rik" "Gm49720" "Ermard"
## [6617] "Chd1" "BC002059" "Gm6712" "Riok2"
## [6621] "Spaca6" "Gm49753" "Vmn1r224" "Gm5145"
## [6625] "Gm19026" "Ppp2r1a" "Zfp160" "Vmn1r234"
## [6629] "Zfp54" "Zfp51" "Zfp948" "Gm31758"
## [6633] "Zfp943" "Zfp758" "Zfp946" "Gm54704"
## [6637] "Gm9805" "Gm7898" "Zscan10" "Bicdl2"
## [6641] "Hcfc1r1" "Srrm2" "Prss32" "Prss21"
## [6645] "Dcpp1" "Dcpp3" "Tmem129" "Rnf7"
## [6649] "Prss27" "BC028777" "Abca3" "Eci1"
## [6653] "Pgp" "Bricd5" "Zfp598" "Noxo1"
## [6657] "Rps2" "Hs3st6" "Mybl1" "Meiob"
## [6661] "Hagh" "Igfals" "Spsb3" "Mrps34"
## [6665] "Nme3" "Ift140" "Clcn7" "Ccdc154"
## [6669] "Uqcc4" "Ppp1r42" "Tsr3" "Tpsg1"
## [6673] "Tekt4" "Lmf1" "Gng13" "Rpusd1"
## [6677] "Ciao3" "Fbxl16" "Wdr24" "Jmjd8"
## [6681] "Cops5" "Mettl26" "Cox7c" "Pgap6"
## [6685] "Axin1" "Luc7l" "Neurl1b" "Atp6v0e"
## [6689] "Bnip1" "Syngap1" "Ggnbp1" "Cpa6"
## [6693] "Itpr3" "Gm10505" "Hmga1" "C130040N14Rik"
## [6697] "Pacsin1" "Snrpc" "Scube3" "Zfp523"
## [6701] "Def6" "E230001N04Rik" "Tram1" "Armc12"
## [6705] "Clpsl2" "Mapk14" "Mapk13" "Srsf3"
## [6709] "Cdkn1a" "BC004004" "Fgd2" "Pim1"
## [6713] "Tbc1d22b" "Lactb2" "Rnf8" "Cmtr1"
## [6717] "Umodl1" "Abcg1" "Ndufv3" "4833413E03Rik"
## [6721] "Cryaa" "Rrp1b" "A530088E08Rik" "Cyp4f37"
## [6725] "Eya1" "Cyp4f15" "Zfp952" "Zfp563"
## [6729] "Myo1f" "Zfp414" "Kank3" "Ndufa7"
## [6733] "Daxx" "Zbtb22" "Tapbp" "Stau2"
## [6737] "Rgl2" "Wdr46" "Vps52" "Rxrb"
## [6741] "Col11a2" "H2-Oa" "H2-DMb2" "Tap1"
## [6745] "Tap2" "H2-Ab1" "Idi1-ps5" "H2-Eb1"
## [6749] "Btnl2" "Notch4" "Gpsm3" "Ager"
## [6753] "Atf6b" "Tnxb" "Nelfe" "Ehmt2"
## [6757] "Neu1" "Anapc1" "Gm5828" "Hspa1l"
## [6761] "Vars1" "Clic1" "Ly6g6c" "Ly6g6e"
## [6765] "D17H6S53E" "Atp6v1g2" "H2-D1" "H2-Q1"
## [6769] "H2-Q2" "Gm49089" "H2-Q3" "H2-Q4"
## [6773] "H2-Q5" "H2-Q6" "Cchcr1" "Psors1c2"
## [6777] "Cdsn" "Flot1" "Nrm" "Ppp1r18"
## [6781] "Jph1" "Dhx16" "Gnl1" "Gm6034"
## [6785] "Gm19684" "Gm6623" "Gm8868" "Trim26"
## [6789] "Polr1has" "Zfp57" "Gabbr1" "Gm6075"
## [6793] "Gm4831" "Or14j6" "Mmut" "Ldha-ps3"
## [6797] "Ptchd4" "Tnfrsf21" "Adgrf5" "Rcan2"
## [6801] "Enpp5" "Runx2os1" "Gm28341" "Supt3"
## [6805] "B230354K17Rik" "Aars2" "Slc35b2" "Gm25008"
## [6809] "Mrpl14" "Mrps18a" "Yipf3" "Lrrc73"
## [6813] "Dlk2" "Mcm3" "Gm55801" "Crip3"
## [6817] "Mrpl2" "Cul7" "Pex6" "Pex39"
## [6821] "Tbcc" "Mrps10" "Mrfap1" "Med20"
## [6825] "Tram2" "Usp49" "Tfeb" "1700067P10Rik"
## [6829] "Trem6l" "Trem2" "Treml1" "Oard1"
## [6833] "Unc5cl" "Lrfn2" "Kif6" "Gm5696"
## [6837] "AY702103" "Plcl2" "Gm9210" "Erh"
## [6841] "Kat2b" "4932415M13Rik" "Gm4471" "Zfp959"
## [6845] "Yju2" "Shd" "Rims1" "Fsd1"
## [6849] "Mpnd" "Chaf1a" "Hdgfl2" "A230051N06Rik"
## [6853] "Mir7b" "Safb" "Catsperd" "Ranbp3"
## [6857] "Dus3l" "Ppp1r14bl" "Acsbg3" "Clpp"
## [6861] "Alkbh7" "Gm17949" "Trip10" "Cntnap5c"
## [6865] "Nudt12os" "Fer" "Gm4701" "Gm23264"
## [6869] "Trappc4" "Gm6420" "Ddx11" "L3mbtl4"
## [6873] "Zbtb14" "Gm9598" "Dlgap1" "Gm16519"
## [6877] "Gm49905" "Spdya" "Wdr43" "Lbh"
## [6881] "Smap1" "Lclat1" "Ehd3" "Spast"
## [6885] "Slc30a6" "Birc6" "Ltbp1" "Gm9360"
## [6889] "Crim1" "Gm18649" "Gpatch11" "Sdhaf4"
## [6893] "Cebpzos" "Qpct" "Rmdn2" "Ttc39d"
## [6897] "Gemin6" "Morn2" "Tmem178" "Gm6594"
## [6901] "Pkdcc" "Mta3" "Spata31e5" "Dync2li1"
## [6905] "Abcg8" "Camkmt" "Six3" "Prkce"
## [6909] "Epas1" "Cript" "Socs5" "Ttc7"
## [6913] "Msh2" "Gm5697" "Rpl36-ps4" "Gm50040"
## [6917] "Gm4832" "Foxn2" "Ppp1r21" "Gm38460"
## [6921] "Gtf2a1l" "Nanp" "Pja2" "Pisd-ps2"
## [6925] "Gm9898" "Tfb1m" "Ldhal6b" "Gm8363"
## [6929] "Serac1" "Fbl" "Ftl1" "Ezr"
## [6933] "Mir692-1" "Gpr31b" "6530411M01Rik" "Phf3"
## [6937] "Qki" "Map3k4" "Slc22a1" "Igf2r"
## [6941] "Mas1" "Pnldc1" "Mrpl18" "Acat3"
## [6945] "Acat2" "Tcte2" "Alyreffm1" "4930474M22Rik"
## [6949] "Wdr27" "Phf10" "Gm7423" "Psmb1"
## [6953] "Gm7177" "Prdm9" "Gm6686" "Rgmb"
## [6957] "Oaz1-ps" "Prim2" "Lnpep" "Gm7535"
## [6961] "Gm49963" "Vmn2r109" "Zfp820" "Gm6540"
## [6965] "Zfp942" "Gm9514" "Zfp944" "Gm16386"
## [6969] "Bag2" "Zfp945" "Casp16" "Zfp213"
## [6973] "Zfp13" "Thoc6" "Tnfrsf12a" "Cldn9"
## [6977] "Paqr4" "Flywch1" "Flywch2" "Psmc5"
## [6981] "Pfdn6" "Gm15455" "Prss33" "Prss41"
## [6985] "Sbpl" "Prss22" "Kctd5" "Amdhd2"
## [6989] "Tbc1d24" "Ccnf" "D330041H03Rik" "E4f1"
## [6993] "Bend6" "Mlst8" "Traf7" "Tsc2"
## [6997] "Npw" "Gfer" "Ndufb10" "Fahd1"
## [7001] "Nubp2" "Eme2" "Jpt2" "Ccdc115"
## [7005] "Cramp1" "Gnptg" "Baiap3" "Ube2i"
## [7009] "Tpsab1" "Cacna1h" "Sox8" "Chtf18"
## [7013] "Gm55306" "Metrn" "Prss40" "Stub1"
## [7017] "Wdr90" "Mcrip2" "Wfikkn1" "Rab40c"
## [7021] "Pigq" "Rab11fip3" "Arhgdig" "Fam234a"
## [7025] "Dusp1" "Fam168b" "Nkx2-5" "Itpr3os"
## [7029] "Uqcc2" "Smim29" "Spdef" "Taf11"
## [7033] "Tead3" "Tulp1" "Fkbp5" "Clps"
## [7037] "Uggt1" "Srpk1" "Bnip5" "Pxt1"
## [7041] "Stk38" "Trp53cor1" "Cpne5" "Ppil1"
## [7045] "Mtch1" "Tmem217b" "Tmem217" "Lman2l"
## [7049] "Ccdc167" "Mdga1" "Gm9937" "Tff3"
## [7053] "Tff1" "Tmprss3" "Rsph1" "U2af1"
## [7057] "Sik1" "Hsf2bp" "Ankrd39" "Notch3"
## [7061] "Akap8" "Akap8l" "Wiz" "Zfp871"
## [7065] "Gm7059" "Zfp870" "Cyp4f41-ps" "Zfp763"
## [7069] "Phf8l" "Sema4c" "Morc2b" "Zfp81"
## [7073] "Zfp101" "Hnrnpm" "Rab11b" "Angptl4"
## [7077] "H2-K2" "H2-K1" "Mir219a-1" "Hsd17b8"
## [7081] "Fam178b" "Slc39a7" "H2-Aa" "Btnl5-ps"
## [7085] "Rnf5" "Egfl8" "C4b" "C4a"
## [7089] "Skic2" "C2" "Hspa1a" "Ilf2"
## [7093] "Actr1b" "Gm10501" "D17H6S56E-5" "Msh5"
## [7097] "Mpig6b" "Ly6g6f" "Gm23442" "Lst1"
## [7101] "Tcf19" "Muc21" "Vars2" "F830112A20Rik"
## [7105] "Gtf2h4" "Tubb5" "Ppp1r18os" "2310061I04Rik"
## [7109] "Atat1" "Abcf1" "H2-T23" "H2-T22"
## [7113] "H2-T10" "Gm20545" "Gm32899" "Rpp21"
## [7117] "Ppp1r11" "Polr1h" "Or2h1" "Or10c1"
## [7121] "Gm25104" "Or14j9" "Or2j3" "AY036118"
## [7125] "Pgk2" "Mgat4a" "Cenpq" "Cd2ap"
## [7129] "Slc25a27" "Runx2" "4930564C03Rik" "Gm4766"
## [7133] "Tmem151b" "Hsp90ab1" "Mymx" "Capn11"
## [7137] "Cracdl" "Tmem63b" "Vegfa" "Rsph9"
## [7141] "Mad2l1bp" "Polr1c" "Tjap1" "Ttbk1"
## [7145] "Cul9" "Srf" "Ptk7" "Tsga10"
## [7149] "Klc4" "Gnmt" "Cnpy3" "Ptcra"
## [7153] "Bicral" "Gm16494" "Taf8" "Bysl"
## [7157] "Tomm6" "Mdfi" "Txndc9" "Gm25201"
## [7161] "Foxp4" "1700122O11Rik" "9830107B12Rik" "A530064D06Rik"
## [7165] "Nfya" "Dazl" "Tbc1d5" "Kcnh8"
## [7169] "Pp2d1" "Aff3" "Sgo1" "Armcx3"
## [7173] "Pot1b" "Stap2" "Sh3gl1" "Ubxn6"
## [7177] "Lrg1" "Sema6b" "Mydgf" "Dpp9"
## [7181] "Chst10" "Ticam1" "Plin3" "Arrdc5"
## [7185] "Ptprs" "Znrf4" "Safb2" "Micos13"
## [7189] "Lonp1" "Vmac" "Nrtn" "Tbc1d8"
## [7193] "Rfx2" "Acsbg2" "Mllt1" "Pspn"
## [7197] "Gtf2f1" "Khsrp" "Slc25a23" "C3"
## [7201] "Gpr108" "Rpl7a-ps5" "Xpo7" "Rnf149"
## [7205] "Pdzph1" "Nudt12" "Fbxl17" "AU016765"
## [7209] "Gm18736" "Rab31" "Twsg1" "Ndufv2"
## [7213] "Mtcl1" "Rab12" "Gm5100" "Ptprm"
## [7217] "Arhgap28" "Tgif1" "Myl12b" "Myl12a"
## [7221] "Emilin2" "Smchd1" "Ndc80" "Trmt61b"
## [7225] "Gm26963" "Creg2" "Xdh" "Memo1"
## [7229] "Atp6v1f" "Gm9351" "Nlrc4" "Fez2"
## [7233] "Strn" "Heatr5b" "Eif2ak2" "Prkd3"
## [7237] "Mfsd9" "Gm49869" "Cdc42ep3" "Cyp1b1"
## [7241] "Hnrnpll" "Srsf7" "Dhx57" "Gm10190"
## [7245] "Sos1" "Rpl31-ps25" "Cox7a2l" "Tgfbrap1"
## [7249] "Kcng3" "Haao" "Zfp36l2" "Thada"
## [7253] "Prepl" "Six3os1" "Six2" "Gm10309"
## [7257] "Stpg4" "Calm2" "Fhl2" "Kcnk12"
## [7261] "Fbxo11" "Lhcgr" "Fshr" "Mettl4"
## [7265] "Gm1976" "Gm23102" "Or10h28" "Cul2"
## [7269] "Gm6235" "Ccdc168" "Lyzl1" "Mtpap"
## [7273] "Rpl7a" "Svil" "BC025933" "Zeb1"
## [7277] "Gm7464" "4921524L21Rik" "Rab18" "Gm18948"
## [7281] "Tex30" "Gm4833" "Fzd8" "Gm7527"
## [7285] "Gm5501" "Thoc1" "Greb1l" "Snrpd1"
## [7289] "Gata6" "Rbbp8" "Rmc1" "Poglut2"
## [7293] "Ttc39c" "Gm50098" "Rsl24d1" "Dsg1b"
## [7297] "4930426D05Rik" "Asxl3" "Dtna" "Mapre2"
## [7301] "Zfp397" "Zfp35" "Txn-ps1" "Galnt1"
## [7305] "2700062C07Rik" "Elp2" "AW554918" "Pik3c3"
## [7309] "B930094E09Rik" "Sap130" "Ammecr1l" "Lims2"
## [7313] "Gm5969" "Gm54825" "Slc40a1" "Ercc3"
## [7317] "Bin1" "Wdr36" "Camk4" "Srp19"
## [7321] "Pkd2l2" "Kif20a" "n-R5s25" "Kdm3b"
## [7325] "Reep2" "Stk-ps2" "Egr1" "Ctnna1"
## [7329] "Snora74a" "Pnet-ps" "Paip2" "Cxxc5"
## [7333] "4930471G03Rik" "Pura" "Cystm1" "Eif4ebp3"
## [7337] "Slc39a10" "Slc35a4" "Ik" "Wdr55"
## [7341] "Zmat2" "Gm6756" "Pcdhb3" "Pcdhb8"
## [7345] "Pcdhb15" "Dele1" "Arhgap26" "Gm28388"
## [7349] "Pabpc2" "Kctd16" "Cstdc7" "Steep1"
## [7353] "Dcp2" "Ythdc2" "1700018A14Rik" "Arl14epl"
## [7357] "Commd10" "Hspe1" "Myo1b" "Gm5236"
## [7361] "Dmxl1" "Tnfaip8" "Fam170a" "Prr16"
## [7365] "Srfbp1" "Zfp474" "Sncaip" "Snx2"
## [7369] "Csnk1g3" "Rpl15" "Gm54362" "Gramd2b"
## [7373] "Phax" "Spmip10" "Gm10536" "Megf10"
## [7377] "Prrc1" "Ccdc192" "Slc27a6" "Adamts19"
## [7381] "Gls" "Minar2" "2610318N02Rik" "Rps14"
## [7385] "Cd74" "Pdgfrb" "Csf1r" "Il17b"
## [7389] "Sh3tc2" "Gm41750" "Htr4" "Nab1"
## [7393] "Apcdd1" "Napg" "St8sia3" "Nedd4l"
## [7397] "Malt1" "Sec11c" "Pmaip1" "Gnal"
## [7401] "Chmp1b" "Impa2" "Inpp1" "Cidea"
## [7405] "Tubb6" "Prelid3a" "Psmg2" "Seh1l"
## [7409] "Cep192" "Ldlrad4" "Rnmt" "A730085E03Rik"
## [7413] "Tcf4" "1700019D03Rik" "Mbd2" "Mex3c"
## [7417] "Mro" "Cxxc1" "Cfap53" "Myo5b"
## [7421] "Acaa2" "Dym" "Gm10532" "Smad2"
## [7425] "Dhrs1" "1700019A02Rik" "Skor2" "Ier3ip1"
## [7429] "Hdhd2" "St8sia5" "Loxhd1" "4930465K10Rik"
## [7433] "Pstpip2" "Epg5" "Pard6g" "Slc66a2"
## [7437] "Stk17b" "Gm17383" "Zfp516" "Ptgr3"
## [7441] "Gm2390" "Cyb5a" "Fbxo15" "Rttn"
## [7445] "Tmx3" "Gm45871" "Zfp438" "Hecw2"
## [7449] "Zeb1os1" "Kif5b" "Odad2" "Mpp7"
## [7453] "Gm9993" "Gm20147" "Ccny" "Cetn1"
## [7457] "Gm17430" "Rock1" "Gm34066" "Esco1"
## [7461] "Abhd3" "Tmem241" "Npc1" "Gm5240"
## [7465] "Zfp521" "Kctd1" "Cdh2" "4921533I20Rik"
## [7469] "Rpl35" "Pgap1" "B4galt6" "Garem1"
## [7473] "Klhl14" "Ccdc178" "Nol4" "Zscan30"
## [7477] "Zfp24" "Ino80c" "Mir187" "Rprd1a"
## [7481] "Ankrd44" "Gm9955" "Tpgs2" "Gm5064"
## [7485] "Rps25" "Bloc1s1" "Gm41780" "Gm7941"
## [7489] "Syt4" "Myo7b" "Proc" "Hspd1"
## [7493] "Gypc" "Stard4" "Nrep" "Epb41l4a"
## [7497] "Gm10548" "Brd8dc" "Brd8" "Cdc23"
## [7501] "Gfra3" "Cdc25c" "Hsfy2" "Etf1"
## [7505] "Sil1" "Slc23a1" "Prob1" "Dnajc18"
## [7509] "Ecscr" "Pfdn1" "Hbegf" "Sra1"
## [7513] "Apbb3" "Satb2" "E230025N22Rik" "Ndufa2"
## [7517] "Hars1" "Gm10545" "Slc25a2" "Taf7"
## [7521] "Uxt" "Hdac3" "Arap3" "1700086O06Rik"
## [7525] "Tyw5" "Pcdh12" "Gnpda1" "Spry4"
## [7529] "Fgf1" "Plac8l1" "Lars1" "Gpr151"
## [7533] "Gm22264" "Mcc" "Gm4839" "Vta1"
## [7537] "Clk1" "Gm10540" "Trim36" "Pggt1b"
## [7541] "Ccdc112" "Mospd4" "Ticam2" "Cdo1"
## [7545] "Atg12" "Gm6883" "Dtwd2" "Ppil3"
## [7549] "Pudp" "Ppic" "Gm8594" "Gm24514"
## [7553] "Gm26959" "Aldh7a1" "C330018D20Rik" "Myoz3"
## [7557] "Synpo" "Ndst1" "Hycc2" "Tcof1"
## [7561] "Slc6a7" "Cdx1" "Hmgxb3" "Afap1l1"
## [7565] "Fech" "Nars1" "Atp8b1" "Gm46618"
## [7569] "Lman1" "Trak2" "Ccbe1" "Afg3l2"
## [7573] "Ptpn2" "Fam210a" "4930503L19Rik" "Poli"
## [7577] "Rpl5" "Gm54867" "Smad4" "Me2"
## [7581] "C2cd6" "Ska1" "Scarna17" "Lipg"
## [7585] "Ctif" "1700003O11Rik" "Katnal2" "Ark2c"
## [7589] "Ark2n" "Haus1" "Siglec15" "Tmem237"
## [7593] "Setbp1" "Adnp2" "Rbfa" "Kcng2"
## [7597] "Ctdp1" "Atp9b" "Sall3" "Zfp236"
## [7601] "Gm54980" "Timm21" "Als2" "Gm7612"
## [7605] "Gnpnat1" "Gm5826" "Socs6" "Mrpl21"
## [7609] "Cpt1a" "1810055G02Rik" "Aldh3b3" "Aldh3b2"
## [7613] "Acy3" "Sumo1" "Tbx10" "Nudt8"
## [7617] "Cabp2" "Cdk2ap2" "Pitpnm1" "Tmem134"
## [7621] "Coro1b" "Ptprcap" "Ppp1ca" "Gm45928"
## [7625] "Ica1l" "Pcx" "Sptbn2" "Rbm4b"
## [7629] "Ccdc87" "Ctsf" "Mrpl11" "Slc29a2"
## [7633] "B4gat1" "Brms1" "Rin1" "Wdr12"
## [7637] "Cd248" "Yif1a" "Gm10817" "Eif1ad"
## [7641] "D330050I16Rik" "AI837181" "1810058N15Rik" "Rela"
## [7645] "Map3k11" "Kcnk7" "Gm37035" "Raph1"
## [7649] "Ltbp3" "Slc25a45" "Syvn1" "Tmem262"
## [7653] "Cdca5" "Lamtor1" "Majin" "Atg2a"
## [7657] "Mir194-2" "Ehd1" "Ino80d" "Men1"
## [7661] "Map4k2" "Pygm" "Trmt112" "Bad"
## [7665] "Ppp1r14b" "Trpt1" "Macrod1" "Gm22113"
## [7669] "Rcor2" "Ndufs1" "Zfta" "Iscu"
## [7673] "Slc22a8" "Chrm1" "Snord22" "Wdr74"
## [7677] "Tmem223" "Hnrnpul2" "Ubxn1" "Ints5"
## [7681] "Prelid1" "Eml3" "Mta2" "Tut1"
## [7685] "Ahnak" "Gm54995" "Rab3il1" "Fads3"
## [7689] "Gm10143" "Syt7" "Cyb561a3" "4933402D24Rik"
## [7693] "Vwce" "Vps37c" "Slc15a3" "Ms4a4b"
## [7697] "Mrpl16" "Patl1" "Gm17802" "Mpeg1"
## [7701] "Rplp1rt" "Or5b21" "Klf7" "Or10q1b"
## [7705] "Or10q12" "Rpl37-ps1" "Gna14" "D030056L22Rik"
## [7709] "Trpm6" "Aldh1a1" "Zfand5" "Abhd17b"
## [7713] "Trpm3" "Fzd5" "Nsa2" "Mir204"
## [7717] "2410080I02Rik" "Gm21542" "Ptar1" "Tmem252"
## [7721] "Cycs" "Dock8" "Gm5249" "Dmrt1"
## [7725] "Akr1cl" "Dmrt3" "Smarca2" "Vldlr"
## [7729] "Plpp6" "Cdc37l1" "Jak2" "Cd274"
## [7733] "Mlana" "Il33" "Uhrf2" "Crygc"
## [7737] "Cstf2t" "A1cf" "Sgms1os1" "Minpp1"
## [7741] "Papss2" "Pten" "Nudt15" "Lipf"
## [7745] "Stambpl1" "Ifit3" "Idh1" "Kif20b"
## [7749] "Gm47773" "Gm9042" "Btaf1" "Marchf5"
## [7753] "Kif11" "Exoc6" "Cyp26c1" "Gm9067"
## [7757] "Cep55" "Txndc12" "Kansl1l" "Gm23300"
## [7761] "Ffar4" "Plce1" "Tbc1d12" "Hells"
## [7765] "Cyp2c55" "Cyp2c66" "Cyp2c29" "Entpd1"
## [7769] "Cc2d2b" "Acadl" "Zfp518a" "Dppa2"
## [7773] "Lcor" "Frat1" "Pgam1" "Zdhhc16"
## [7777] "Ankrd2" "4933411K16Rik" "Pi4k2a" "Marveld1"
## [7781] "Rpl31-ps14" "Zfyve27" "Golga7b" "R3hcc1l"
## [7785] "Cnnm1" "Nkx2-3" "Cutc" "Scd3"
## [7789] "Scd2" "Hif1an" "Pax2" "Erbb4"
## [7793] "Gm5246" "Slf2" "Sema4g" "Twnk"
## [7797] "Sfxn3" "Tlx1" "Dpcd" "4930505N22Rik"
## [7801] "Pprc1" "Nolc1" "Gm8840" "Nfkb2"
## [7805] "Fbxl15" "Mir146b" "Mfsd13a" "Trim8"
## [7809] "Sfxn2" "Taf5" "Neurl1a" "Slk"
## [7813] "Sfr1" "Bard1" "Gsto2" "Cfap58"
## [7817] "Rpl31-ps18" "Ins1" "Add3" "Smc3"
## [7821] "Rbm20" "Shoc2" "Acsl5" "Vti1a"
## [7825] "Gm8870" "Tcf7l2" "Casp7" "Nhlrc2"
## [7829] "Adrb1" "Fhip2a" "Gm50185" "Ccdc172"
## [7833] "Gm9276" "Slc18a2" "Emx2" "Fn1"
## [7837] "E330013P04Rik" "Nanos1" "Dennd10" "Grk5"
## [7841] "Gm25431" "Gm50307" "Ppp6r3" "Lrp5"
## [7845] "Tcirg1" "Ndufs8" "Gm5829" "Aldh3b1"
## [7849] "Ndufv1" "Gstp1" "Aip" "Rps6kb2"
## [7853] "Tbc1d10c" "Rad9a" "Ssh3" "Rhod"
## [7857] "Lrfn4" "Mreg" "Rbm14" "Dpp3"
## [7861] "Peli3" "Npas4" "Tmem151a" "Rab1b"
## [7865] "Klc2" "Pacs1" "Sf3b2" "Banf1"
## [7869] "Aup1" "Marchf4" "Sart1" "Tsga10ip"
## [7873] "Gm6293" "Ccdc85b" "Mus81" "Snx32"
## [7877] "Nscme3l" "Kat5" "Pcnx3" "Ehbp1l1"
## [7881] "Igfbp5" "Malat1" "Frmd8" "Tigd3"
## [7885] "Cdc42ep2" "Pola2" "Tm7sf2" "Zfpl1"
## [7889] "Snx15" "Arl2" "Slc22a12" "Tnp1"
## [7893] "Gm14964" "Rps6ka4" "Ccdc88b" "Catsperz"
## [7897] "Kcnk4" "Plcb3" "Fkbp2" "Dnajc4"
## [7901] "Nudt22" "Fermt3" "Tns1" "Stip1"
## [7905] "Otub1" "Cox8a" "Mark2" "Spindoc"
## [7909] "Slc3a2" "Tmem179b" "Taf6l" "Polr2g"
## [7913] "Ttc9c" "Aamp" "Gng3" "Uqcc3"
## [7917] "5730408K05Rik" "Rom1" "Incenp" "Best1"
## [7921] "Gm50359" "Fen1" "Myrf" "Lrrc10b"
## [7925] "Tmbim1" "Sdhaf2" "Tmem138" "Cd5"
## [7929] "Tmem132a" "Tmem109" "Zp1" "Ccdc86"
## [7933] "Ms4a15" "Ms4a20" "Ms4a19" "Zfp142"
## [7937] "Ms4a13" "Ms4a5" "Ms4a14" "Or10q3"
## [7941] "Gm6365" "Or5bb10" "Or5an1c" "Or5a21"
## [7945] "Dtx4" "Or5b125-ps1" "Rnf25" "Or9q2"
## [7949] "Tle4" "Psat1" "Foxb2" "Ostf1"
## [7953] "Gm22684" "Anxa1" "Aldh1a7" "Tmc1"
## [7957] "Gda" "Prkag3" "Cfap95" "Entrep1"
## [7961] "Fxn" "Pabir1" "Zng1" "Gm34432"
## [7965] "Pum3" "Rfx3" "Glis3" "Insl6"
## [7969] "Fev" "Ermp1" "Brd10" "Ranbp6"
## [7973] "Ppp1r2-ps3" "Dkk1" "Prkg1" "Asah2"
## [7977] "Rnls" "Lipo3" "Ankrd22" "Zranb1"
## [7981] "Cryba2" "Acta2" "Lipa" "Pank1"
## [7985] "Mir107" "Ankrd1" "F530104D19Rik" "Fgfbp3"
## [7989] "Cpeb3" "Myof" "Rbp4" "Cfap65"
## [7993] "Fra10ac1" "Ctdspl2" "Pdlim1" "Sorbs1"
## [7997] "Aldh18a1" "Tctn3" "Pik3ap1" "Rrp12"
## [8001] "Exosc1" "Mms19" "Ihh" "Morn4"
## [8005] "Avpi1" "Crtac1" "Loxl4" "Pyroxd2"
## [8009] "Got1" "Dnmbp" "Cpn1" "Cyp2c23"
## [8013] "Erlin1" "Cnppd1" "Chuk" "Cwf19l1"
## [8017] "Bloc1s2" "Pkd2l1" "Scd1" "Ndufb8"
## [8021] "Pdzd7" "Lbx1" "Poll" "Fbxw4"
## [8025] "Abcb6" "Fgf8" "Oga" "Kcnip2"
## [8029] "Armh3" "Pitx3" "Psd" "Cuedc2"
## [8033] "2310034G01Rik" "Actr1a" "Arl3" "Atg9a"
## [8037] "Cyp17a1" "Pcgf6" "Calhm3" "Sh3pxd2a"
## [8041] "Stn1" "Col17a1" "Cfap43" "Itprip"
## [8045] "1700001K23Rik" "Smndc1" "Tuba4a" "Mirt1"
## [8049] "Gucy2g" "Zdhhc6" "Dclre1a" "Ccdc186"
## [8053] "Ablim1" "Gfra1" "Hspa12a" "Shtn1"
## [8057] "Vax1" "Dnpep" "Pdzd8" "Fam204a"
## [8061] "Eif3a" "Sfxn4" "Prdx3" "Zfp950"
## [8065] "Mplkipl1" "Csf2ra" "Lax1" "Fam171a1"
## [8069] "Obsl1" "Dclre1c" "Phxr1" "Cdnf"
## [8073] "Fam107b" "Frmd4a" "Gm10862" "Bend7"
## [8077] "Sephs1" "Phyh" "Ccdc3" "Pax3"
## [8081] "Nudt5" "Usp6nl" "Gata3os" "C630004M23Rik"
## [8085] "Kin" "Itih5" "Mir669b" "Mir297b"
## [8089] "Gm10851" "Il2ra" "Ube2g1" "BC031181"
## [8093] "Farsb" "Il15ra" "Ankrd16" "Stam"
## [8097] "Mrc1" "Cacnb2" "Arl5b" "Gm13365"
## [8101] "Plxdc2" "Gm25147" "Spag6" "BC035947"
## [8105] "4930426L09Rik" "Msrb2" "1810010K12Rik" "Otud1"
## [8109] "Etl4" "Gad2" "1700092C17Rik" "Apbb1ip"
## [8113] "Pdss1" "Acbd5" "Wdfy1" "Yme1l1"
## [8117] "Ankrd68" "Gm13410" "Il1rn" "Dph7"
## [8121] "Nsmf" "Tmem203" "Tprn" "Tmem210"
## [8125] "Lrrc26" "Serpine2" "Man1b1" "Sapcd2"
## [8129] "Entpd2" "Npdc1" "Abca2" "Clic3"
## [8133] "Edf1" "Fcnaos" "Bmyc" "Dipk1b"
## [8137] "Slc25a5" "Surf2" "Stkld1" "Cacfd1"
## [8141] "Gm13397" "Adamtsl2" "Rxra" "Ppp1r26"
## [8145] "Gbgt1" "Gm10134" "Ralgds" "Fam124b"
## [8149] "Ddx31" "Ttf1" "Med27" "Rapgef1"
## [8153] "Gm13547" "Coq4" "Slc27a4" "Cercam"
## [8157] "Tbc1d13" "Endog" "Gm17764" "Lrrc8a"
## [8161] "Phyhd1" "Dolpp1" "Ptpa" "Ntmt1"
## [8165] "Tor1b" "Gpr107" "Ncs1" "Hmcn2"
## [8169] "Fubp3" "Sphkap" "Exosc2" "Abl1"
## [8173] "Aif1l" "Plpp7" "Pomt1" "Golga2"
## [8177] "Ciz1" "Naif1" "Eeig1" "Pip5kl1"
## [8181] "Slc16a14" "St6galnac6" "Ak1" "Eng"
## [8185] "Tor2a" "Gm24165" "Niban2" "Angptl2"
## [8189] "Cntrl" "Gsn" "Glo1" "Ncl"
## [8193] "Morn5" "Mrrf" "Or1n2" "Lhx2"
## [8197] "Gm25081" "Gm13588" "Olfml2a" "Wdr38"
## [8201] "Gm13456" "Acvr2a" "Tmem165" "Alppl2"
## [8205] "Mbd5" "Epc2" "Kif5c" "Lypd6b"
## [8209] "Gm13498" "Rif1" "Arl6ip6" "Gm25489"
## [8213] "Gpd2" "Pkp4" "Ngef" "Dapl1"
## [8217] "Ldha-ps" "Tank" "Psmd14" "Gca"
## [8221] "Scn2a" "Csrnp3" "Tax1bp3" "4933409G03Rik"
## [8225] "Cers6" "Usp40" "Ppig" "Ssb"
## [8229] "Ubr3" "Myo3b" "Sp5" "Gad1"
## [8233] "Dcaf17" "Hat1" "Metap1d" "Platr26"
## [8237] "Dnajb3" "Itga6" "Pdk1" "Rapgef4"
## [8241] "Map3k20" "Cdca7" "Ak4" "Sp3os"
## [8245] "Sp9" "Scrn3" "Hoxd13" "Glrp1"
## [8249] "Hoxd10" "Hoxd8" "Hoxd4" "Hoxd1"
## [8253] "Mtx2" "Agps" "Rbm45" "Ube2e3"
## [8257] "Itprid2" "Prdx6b" "Arl4c" "Dnajc10"
## [8261] "Gm13687" "Dusp19" "Nup35" "Gm13675"
## [8265] "Fsip2" "Itgav" "Med19" "Ypel4"
## [8269] "Timm10" "Gbx2" "Ssrp1" "Tnks1bp1"
## [8273] "Gm13735" "Or12e8" "Mtch2" "C1qtnf4"
## [8277] "Kbtbd4" "Celf1" "Rapsn" "Psmc3"
## [8281] "Iqca1" "Mybpc3" "Acp2" "Pacsin3"
## [8285] "Arhgap1" "Harbi1" "Ambra1" "Gm9821"
## [8289] "Phf21a" "Pex16" "Frey1" "Col6a3"
## [8293] "Chst1" "Syt13" "Alkbh3os1" "2810002D19Rik"
## [8297] "Commd9" "Pamr1" "Slc1a2" "Apip"
## [8301] "Lmo2" "Cd59b" "Rab17" "Cd59a"
## [8305] "A930018P22Rik" "Gm13882" "Ccdc73" "Wt1"
## [8309] "Immp1l" "Gm9342" "Kif18a" "Bdnf"
## [8313] "Lin7c" "Mrpl43" "Ilkap" "Lgr4"
## [8317] "Ccdc34" "Gm13961" "Or4k36" "Or4g7"
## [8321] "Lpcat4" "Nop10" "Gm21985" "Katnbl1"
## [8325] "Aven" "Hes6" "Tmco5b" "Cdin1"
## [8329] "Tmco5" "Spred1" "Mir674" "Gm25189"
## [8333] "Fam98b" "Bub1b" "Inafm2" "Knstrn"
## [8337] "Per2" "Bahd1" "Rad51" "Gm14137"
## [8341] "Zfyve19" "Spint1" "Vps18" "Chac1"
## [8345] "Chp1" "Nusap1" "Itpka" "Hdac4"
## [8349] "Mga" "Mapkbp1" "Snap23" "Haus2"
## [8353] "Stard9" "AV039307" "Tmem62" "Ccndbp1"
## [8357] "Adal" "Map1a" "Ndufa10" "Ckmt1"
## [8361] "Hypk" "Wdr76" "Golm2" "B2m"
## [8365] "Terb2" "Afg2b" "AA467197" "Bloc1s6"
## [8369] "Sqor" "Cops9" "Sema6d" "Dut"
## [8373] "Eid1" "Dtwd1" "Ap4e1" "Stard7"
## [8377] "Adra2b" "Mrps5" "Acoxl" "Spdye4c"
## [8381] "Otos" "Mertk" "Fbln7" "Zc3h6"
## [8385] "Polr1b" "Chchd5" "Il1bos" "Sirpa"
## [8389] "Stk35" "Tgm3" "Nop56" "Ankmy1"
## [8393] "Snord57" "Ebf4" "1700020A23Rik" "Tmem239"
## [8397] "Vps16" "Ptpra" "Mrps26" "Oxt"
## [8401] "Itpa" "Atrn" "9430060I03Rik" "Ap5s1"
## [8405] "Pank2" "Mir103-2" "Smox" "Prnp"
## [8409] "Prn" "Cds2" "Chgb" "Mcm8"
## [8413] "Plcb1" "Kif1a" "Plcb4" "Ankef1"
## [8417] "Slx4ip" "Btbd3" "Macrod2" "Snrpb2"
## [8421] "Dstn" "Banf2" "Mgme1" "Kat14"
## [8425] "Mrpl52" "Mab21l4" "Zfp133-ps" "Polr3f"
## [8429] "Sec23b" "Dtd1" "Scp2d1" "Slc24a3"
## [8433] "Naa20" "Cfap61" "Insm1" "Xrn2"
## [8437] "Pask" "6430503K07Rik" "Gm14113" "Gm14106"
## [8441] "A530006G24Rik" "Nxt1" "Cstl1" "Cstdc1"
## [8445] "Cst12" "Cst8" "Cst13" "Thap4"
## [8449] "Cst9" "Fndc10l" "Syndig1" "Entpd6"
## [8453] "Pygb" "Gins1" "Gm14149" "Gm14148"
## [8457] "Nsfl1c" "Fkbp1a" "Pdcd1" "Sdcbp2"
## [8461] "Angpt4" "Scrt2" "Tcf15" "Csnk2a1"
## [8465] "Gm14165" "6820408C15Rik" "Defb20" "Defb21"
## [8469] "Defb36" "Gm5264" "Mcts2" "Gm14162"
## [8473] "Cox4i2" "Tpx2" "Ttll9" "Xkr7"
## [8477] "Ccm2l" "Hck" "Tm9sf4" "Kif3b"
## [8481] "Slco6b1" "Asxl1" "Dnmt3b" "Tomm20"
## [8485] "Bpifb2" "Bpifb3" "Bpifa3" "Bpifb5"
## [8489] "Cbfa2t2" "1700003F12Rik" "Actl10" "Slco6c1"
## [8493] "Zfp341" "Chmp4b" "Raly" "a"
## [8497] "Dynlrb1" "Map1lc3a" "Trp53inp2" "Acss2"
## [8501] "Myh7b" "Procr" "Macir" "Cep250"
## [8505] "Spag4" "Romo1" "Cnbd2" "Epb41l1"
## [8509] "Aar2" "Dlgap4" "Myl9" "Tgif2"
## [8513] "Rab5if" "Pam" "Src" "Nnat"
## [8517] "Ctnnbl1" "Vstm2l" "Rprd1b" "Bpi"
## [8521] "Lbp" "Adig" "Arhgap40" "Slc32a1"
## [8525] "Pign" "Ppp1r16b" "Fam83d" "4933416E03Rik"
## [8529] "Top1" "Plcg1" "Lpin3" "Gm14243"
## [8533] "Gm11452" "L3mbtl1" "Sgk2" "Cdv3"
## [8537] "Bcl2" "Ift52" "Mybl2" "Tox2"
## [8541] "Gdap1l1" "Hnf4a" "Ttpal" "Pkig"
## [8545] "Ccn5" "Kcnk15" "Ywhab" "Kdsr"
## [8549] "Pabpc1l" "Svs5" "Dbndd2" "Pigt"
## [8553] "Dnttip1" "Ube2c" "Snx21" "Zswim3"
## [8557] "Zswim1" "Ctsa" "Vps4b" "Pcif1"
## [8561] "Cd40" "Ncoa3" "Trp53rkb" "Arfgef2"
## [8565] "Ddx27" "Zfas1" "Slc9a8" "Cebpb"
## [8569] "A530013C23Rik" "Tsn" "Ptpn1" "Mocs3"
## [8573] "Tshz2" "Hax1" "Pfdn4" "Fam210b"
## [8577] "Cstf1" "Rtf2" "Tfap2c" "Spo11"
## [8581] "Inhbb" "Rbm38" "Pck1" "Cimip1"
## [8585] "Rab22a" "1700010B08Rik" "Stx16" "Nelfcd"
## [8589] "Tubb1" "Gm14439" "Gm14296" "Tmem177"
## [8593] "Gm14403" "Zfp971" "Fam217b" "Cdh26"
## [8597] "Wtap" "4930591A17Rik" "Cdh4" "Lsm14b"
## [8601] "Ss18l1" "Osbpl2" "Cfap221" "Adrm1"
## [8605] "Rps21" "Gata5os" "Mrgbp" "Ogfr"
## [8609] "Col9a3" "Gid8" "Slc17a9" "Arfgap1"
## [8613] "Ppdpf" "Tmem37" "Fndc11" "Rtel1"
## [8617] "Zgpat" "Slc2a4rg-ps" "Abhd16b" "Tpd52l2"
## [8621] "Dnajc5" "Prpf6" "Tcea2" "Oprl1"
## [8625] "Dbi" "Myt1" "Pcmtd2" "Polr3k"
## [8629] "Gm5466" "Rpp38" "Suv39h2" "Prpf18"
## [8633] "Optn" "Camk1d" "Sec61a2" "Marco"
## [8637] "Proser2" "Gm13384" "Echdc3" "Gm10855"
## [8641] "Slc25a36" "Gata3" "Taf3" "Atp5f1c"
## [8645] "Itih2" "Pfkfb3" "Ncstn" "Insig2"
## [8649] "Rbm17" "Fbh1" "Gm13310" "Itga8"
## [8653] "Mindy3" "C1ql3" "Rsu1" "St8sia6"
## [8657] "Nsun6" "H2al2a" "Htr5b" "Dnajc1"
## [8661] "Pip4k2a" "4921504E06Rik" "Arhgap21" "Gm13377"
## [8665] "Enkur" "Abi1" "Mastl" "Spopl"
## [8669] "Pax8" "Ddx18" "Gm13416" "Cacna1b"
## [8673] "Noxa1" "Tor4a" "Nelfb" "Stpg3"
## [8677] "Slc34a3" "Ssna1" "Uap1l1" "Paxx"
## [8681] "Nckap5" "Ptgds" "Lcn12" "Traf2"
## [8685] "Phpt1" "Ajm1" "Rabl6" "Ccdc183"
## [8689] "Fcna" "Sohlh1" "Camsap1" "Rpl27a"
## [8693] "Ubac1" "Nacc2" "Qsox2" "Ccdc187"
## [8697] "Card9" "Snapc4" "Notch1" "Gm13359"
## [8701] "Surf6" "Med22" "Tmem163" "Surf1"
## [8705] "Rexo4" "Mymk" "Fam163b" "Sardh"
## [8709] "Vav2" "Brd3" "Gm13372" "Pierce1"
## [8713] "Gtf3c5" "Zranb3" "Gfi1b" "Spaca9"
## [8717] "Gtf3c4" "Barhl1" "Cfap77" "Trub2"
## [8721] "2600006K01Rik" "Dync2i2" "Zdhhc12" "Spout1"
## [8725] "Mcm6" "Kyat1" "1700084E18Rik" "Dolk"
## [8729] "1700001O22Rik" "Asb6" "BC005624" "Fnbp1"
## [8733] "Qrfp" "Fibcd1" "Swi5" "Cxcr4"
## [8737] "Dnm1" "Bbln" "Lcn2" "Slc25a25"
## [8741] "9430097D07Rik" "Cdk9" "Ttc16" "Cfap157"
## [8745] "Stxbp1" "Lrsam1" "Cd55b" "Slc2a8"
## [8749] "Garnl3" "Zbtb43" "Lmx1b" "Pbx3"
## [8753] "Gapvd1" "Rabepk" "Fbxw2" "Psmd5"
## [8757] "Phf19" "Ctbp1" "Cd55" "Traf1"
## [8761] "4930568D16Rik" "Rbm18" "Gm13436" "Or12k8"
## [8765] "Or1b1" "Pdcl" "Zbtb6" "Zbtb26"
## [8769] "Strbp" "Il24" "Psmb7" "Nr5a1"
## [8773] "Golga1" "Ppp6c" "Gm13458" "Zeb2"
## [8777] "Orc4" "Mmadhc" "Gm13487" "Rnd3"
## [8781] "Mapkapk2" "Rbm43" "Arl5a" "Cacnb4"
## [8785] "Stam2" "Prpf40a" "Gm13501" "Rprm"
## [8789] "Gm13531" "Cytip" "Acvr1" "Rassf5"
## [8793] "Ccdc148" "Baz2b" "Gm13570" "Cd302"
## [8797] "Rbms1" "Gm13576" "Grb14" "Cobll1"
## [8801] "Ttc21b" "Scn7a" "Ikbke" "Spc25"
## [8805] "Abcb11" "Cfap210" "Mettl5" "Gm26558"
## [8809] "Tlk1" "Mettl8" "Slc25a12" "Dlx2"
## [8813] "Eif1-ps3" "Mfsd4a" "Ola1" "Chn1"
## [8817] "Atp5mc3" "Gm13668" "Lnpk" "Mrpl23"
## [8821] "Evx2" "Hoxd3os1" "Haglr" "Nfe2l2"
## [8825] "Tmcc2" "Ift70b" "Ift70a1" "Prkra"
## [8829] "Fkbp7" "Ttn" "Sestd1" "Zfp385b"
## [8833] "Cwc22" "Cerkl" "Pde1a" "Cntn2"
## [8837] "Frzb" "Rps4x" "Zswim2" "Calcrl"
## [8841] "Tfpi" "Selenoh" "Clp1" "Serping1"
## [8845] "Smtnl1" "Rtn4rl2" "Gm26616" "P2rx3"
## [8849] "Lrrc55" "Gm13719" "Or5d16" "Or5d44"
## [8853] "Or4c119" "Or4c121" "Or4c58" "Or4b13"
## [8857] "Or4b1b" "Sox13" "Ptprj" "Ndufs3"
## [8861] "Ptpmt1" "Slc39a13" "Madd" "Nr1h3"
## [8865] "Ddb2" "Zfp408" "Atg13" "Dgkz"
## [8869] "Abhd16a" "Snrpe" "Creb3l1" "Large2"
## [8873] "Mapk8ip1" "Cry2" "Prdm11" "Tspan18"
## [8877] "Cd82" "Ext2" "Gm13889" "Hsd17b12"
## [8881] "Atp2b4" "Mir670hg" "Ttc17" "Api5"
## [8885] "Iftap" "Fjx1" "Pdhx" "Ehf"
## [8889] "Cat" "4931422A03Rik" "D430041D05Rik" "Prelp"
## [8893] "Tcp11l1" "Eif3m" "Wt1os" "Rcn1"
## [8897] "Elp4" "Arl14ep" "Mettl15" "Gm13937"
## [8901] "Bbox1" "Or4k35" "Btg2" "Nutm1"
## [8905] "Ryr3" "Scg5" "Arhgap11a" "Actc1"
## [8909] "Zfp770" "Dph6" "Rab5b" "Fsip1"
## [8913] "Srp14" "Ppfia4" "Bmf" "Plcb2"
## [8917] "Ccdc9b" "Rmdn3" "Dnajc17" "Ino80"
## [8921] "Exd1" "Oip5" "Ltk" "Ndufaf1"
## [8925] "Mgat4e" "Rpap1" "Gm13998" "Gm13999"
## [8929] "Ehd4" "Pla2g4d" "Tmem87a" "Zfp106"
## [8933] "Lrrc57" "Cdan1" "Ttbk2" "Ppp1r12b"
## [8937] "Ubr1" "Lcmt2" "Zscan29" "Ell3"
## [8941] "Mageb3" "Patl2" "Shf" "Slc30a4"
## [8945] "Myef2" "Fbn1" "Ptprv" "Cep152"
## [8949] "Secisbp2l" "Cops2" "Fam227b" "Hdc"
## [8953] "Trpm7" "Sppl2a" "Ncaph" "1810024B03Rik"
## [8957] "Gm10766" "Gpr37l1" "Kcnip3" "Zfp661"
## [8961] "Mal" "Mall" "Mtln" "Bub1"
## [8965] "Morrbid" "Gm14006" "Ckap2l" "Gm25703"
## [8969] "Rnpep" "Cpxm1" "4930473A02Rik" "Avp"
## [8973] "Lzts3" "Ddrgk1" "Gfra4" "Adam33"
## [8977] "Siglec1" "Spef1" "Cenpb" "Sar1a"
## [8981] "Timm17a" "Rnf24" "Adra1d" "Rassf2"
## [8985] "Tmem230" "Pcna" "Lrrn4" "Tmx4"
## [8989] "Gm14053" "Jag1" "Rps19-ps7" "Nav1"
## [8993] "Esf1" "Sel1l2" "Gm23846" "Bfsp1"
## [8997] "Rrbp1" "Gm5535" "Snx5" "Ovol2"
## [9001] "Dzank1" "Rbbp9" "Pkp1" "Crnkl1"
## [9005] "Nkx2-4" "Nkx2-2" "Gm14115" "Thbd"
## [9009] "Cd93" "Cstdc2" "Cst3" "Gm10750"
## [9013] "C530025M09Rik" "Mroh3" "Zfp1001" "3300002I08Rik"
## [9017] "Gm14122" "Zfp442" "Apmap" "Acss1"
## [9021] "Abhd12" "Ninl" "4921509C19Rik" "Snph"
## [9025] "Inava" "Psmf1" "Fam110a" "Rbck1"
## [9029] "Trib3" "Sox12" "Defb29" "Defb19"
## [9033] "Defb45" "Defb25" "Foxs1" "Nek7"
## [9037] "Dusp15" "Pdrg1" "Plagl2" "Nol4l"
## [9041] "Commd7" "Sun5" "Cdk5rap1" "Necab3"
## [9045] "Pxmp4" "4930519P11Rik" "Cfhr1" "Eif2s2"
## [9049] "Ncoa6" "Gm14239" "Gss" "Edem2"
## [9053] "Eif6" "Fam83c" "Uqcc1" "Gdf5"
## [9057] "6430550D23Rik" "Cfhr3" "Nfs1" "Scand1"
## [9061] "Pdcd10" "Norad" "5730471H19Rik" "4930518I15Rik"
## [9065] "Sla2" "Dsn1" "Mtcl2" "Samhd1"
## [9069] "Cfh" "Ghrh" "Blcap" "Tti1"
## [9073] "Tgm2" "D630003M21Rik" "Gm826" "Mafb"
## [9077] "Chd6" "Ptprt" "Gm56286" "Gm4845"
## [9081] "Gm11453" "Gtsf1l" "Jph2" "Fitm2"
## [9085] "Hnf4aos" "Ada" "Rims4" "Tomm34"
## [9089] "Wfdc5" "Wfdc15a" "Gm12902" "Ro60"
## [9093] "Matn4" "Trp53tg5" "Wfdc6a" "Eppin"
## [9097] "Wfdc11" "Wfdc3" "Tnnc2" "Spata25"
## [9101] "Pltp" "4930445K14Rik" "Rgs2" "Zfp335"
## [9105] "Cdh22" "Slc35c2" "Elmo2" "Zfp334"
## [9109] "Ocstamp" "Slc13a3" "Trp53rka" "Zmynd8"
## [9113] "Sulf2" "Pla2g4a" "Znfx1" "Gm11472"
## [9117] "Kcnb1" "Ptgis" "B4galt5" "Spata2"
## [9121] "Peds1" "Ripor3" "Kcng1" "Atp9a"
## [9125] "Bex4" "Sall4" "Zfp64" "Zfp217"
## [9129] "Bcas1" "Cbln4" "Aurka" "Bmp7"
## [9133] "Zbp1" "Pmepa1" "Ppp4r1l-ps" "Odr4"
## [9137] "Mir296" "Ctsz" "Atp5f1e" "Prelid3b"
## [9141] "Gm14407" "Ppp1r3d" "Taf4" "Psma7"
## [9145] "Cables2" "Gata5" "Hmcn1" "Gm14340"
## [9149] "Nkain4" "Eef1a2" "Gmeb2" "Arfrp1"
## [9153] "Zfp512b" "Sox18" "Rgs19" "Gm2077"
## [9157] "Zc2hc1a" "Gm10138" "Gm7103" "Gm5841"
## [9161] "Myef2l" "Lrrcc1" "E2f5" "Car2"
## [9165] "Cypt12" "Gm7442" "Cp" "Hltf"
## [9169] "Swt1" "Tbl1xr1" "Rprl2" "Spin3-ps"
## [9173] "Spata16" "Tnfsf10" "Ghsr" "Pld1"
## [9177] "Tnik" "Slc2a2" "Gm1527" "Rnf2"
## [9181] "Mir551b" "Mynn" "Lrriq4" "Sec62"
## [9185] "Gpr160" "Skil" "Cldn11" "Kcnmb2"
## [9189] "Zfp639" "Actl6a" "Cox7b" "Ndufb5"
## [9193] "Ttc14" "Gm5708" "Sox2" "Gm7741"
## [9197] "Acad9" "Exosc9" "Bltp1" "Gm12582"
## [9201] "Fgf2" "Golga7" "Mir6942" "1700025G04Rik"
## [9205] "Afg2a" "Rps23" "Fat4" "Intu"
## [9209] "Plk4" "Gm22043" "Larp1b" "D3Ertd751e"
## [9213] "Pcdh10" "Gm20557" "Tsen15" "4930577N17Rik"
## [9217] "Mgst2" "Gm10729" "Foxo1" "Lhfpl6"
## [9221] "Proser1" "Postn" "Alg5" "Smad9"
## [9225] "Spart" "Rgl1" "Ccdc169" "Sohlh2"
## [9229] "Tm4sf4" "Eif2a" "Selenot" "Gm9696"
## [9233] "Mbnl1" "Rap2b" "Mme" "Kcnab1"
## [9237] "Gm7278" "Gm54743" "Acsf2" "Tiparp"
## [9241] "Gm5847" "Lekr1" "Gm6555" "Rsrc1"
## [9245] "Mfsd1" "Smc4" "Mir15b" "Lamc1"
## [9249] "Ppm1l" "Nmd3" "Gm8604" "Serpini1"
## [9253] "Spmip2" "4930589L23Rik" "Ppid" "4930579G24Rik"
## [9257] "Ctso" "Asic5" "Npl" "Sfrp2"
## [9261] "Gm7115" "Gatb" "Higd1a" "Gm25188"
## [9265] "Lrba" "Gm25039" "Cd1d2" "Etv3"
## [9269] "Etv3l" "Rgsl1" "Hdgf" "Gpatch4"
## [9273] "Mef2d" "Glmp" "Smg5" "Paqr6"
## [9277] "Ubqln4" "Ssr2" "Gon4l" "Gm23054"
## [9281] "Teddm2" "Pklr" "Gm45927" "Entrep3"
## [9285] "Gba1" "Thbs3" "Muc1" "Krtcap2"
## [9289] "Dpm3" "Dcst2" "Shc1" "Ier5"
## [9293] "Pygo2" "Pmvk" "Ube2q1" "4933434E20Rik"
## [9297] "Tpm3" "Nup210l" "Rab13" "Jtb"
## [9301] "Slc39a1" "Crtc2" "Mr1" "Gatad2b"
## [9305] "S100a13" "S100a7a" "Pglyrp3" "Sprr2a3"
## [9309] "Sprr2d" "Gm18432" "Flg" "Tchh"
## [9313] "Tdpoz3" "Gm20695" "Gm5532" "Spopfm2"
## [9317] "Them4" "Rorc" "Lingo4" "Tdrkh"
## [9321] "Celf3" "Selenbp2" "Selenbp1" "Vps72"
## [9325] "Tmod4" "Lhx4" "Cers2" "Arnt"
## [9329] "Ctss" "Golph3l" "Ensa" "Mcl1"
## [9333] "H2bc21" "Gm24136" "Hjv" "Txnip"
## [9337] "Cep350" "Ankrd34a" "Lix1l" "Rbm8a"
## [9341] "Pex11b" "Itga10" "Ankrd35" "Rnf115"
## [9345] "Pdzk1" "Gja5" "Acp6" "Tor1aip1"
## [9349] "Fmo5" "Prkab2" "Notch2" "Adam30"
## [9353] "Gm12474" "Vtcn1" "Trim45" "Igsf3"
## [9357] "Tspan2" "Sike1" "Axdnd1" "Ampd1"
## [9361] "Bcas2" "Syt6" "Rhoc" "4930564D02Rik"
## [9365] "Inka2" "Adora3" "Wdr77" "Ovgp1"
## [9369] "Lrif1" "Soat1" "Kcna3" "Kcna2"
## [9373] "Alx3" "Eps8l3" "Gnat2" "Amigo1"
## [9377] "Taf13" "Clcc1" "Aknad1" "Slc25a54"
## [9381] "Tor3a" "Slc25a24" "Gm9889" "Dph5"
## [9385] "Extl2" "Dbt" "Sass6" "Gm29736"
## [9389] "Plppr5" "Dpyd" "Alg14" "Fam20b"
## [9393] "Cnn3" "Gclm" "Dnttip2" "Bcar3"
## [9397] "Pde5a" "Arln" "Sec24d" "Gm9372"
## [9401] "Gm22575" "Ndst4" "Ralgps2" "Camk2d"
## [9405] "Zgrf1" "Neurog2" "Tifa" "Elovl6"
## [9409] "Pla2g12a" "Casp6" "Col25a1" "Lef1"
## [9413] "Papss1" "Tex35" "Ints12" "Ppa2"
## [9417] "Cxxc4" "Gm55241" "Cenpe" "Slc9b1"
## [9421] "Ube2d3" "Manba" "Slc39a8" "Ppp3ca"
## [9425] "Micall1" "Brinp2" "Ddit4l" "Dnajb14"
## [9429] "Trmt10a" "Adh7" "Adh1" "Adh4"
## [9433] "Adh5" "Eif4e" "Mir1956" "Kyat3"
## [9437] "Gm7430" "Odf2l" "Znhit6" "Ddah1"
## [9441] "Gm6525" "Bcl10" "2410004B18Rik" "Syde2"
## [9445] "Lpar3" "Ssx2ip" "Ctbs" "4930562F07Rik"
## [9449] "Gng5" "Ttll7" "Gm5149" "Fubp1"
## [9453] "Usp33" "Zzz3" "Pigk" "Slc44a5"
## [9457] "Cryz" "Lrriq3" "Cacybp" "Scp2-ps1"
## [9461] "Negr1" "Zranb2" "1810013D15Rik" "Ankrd13c"
## [9465] "Gm22944" "Gm6140" "Pex2" "Gm6194"
## [9469] "Hey1" "Gpr52" "Mrps28" "Zfp704"
## [9473] "Gm17877" "Zfand1" "Snx16" "Gm21631"
## [9477] "Rbis" "Gm16399" "Gm5150" "Gm56811"
## [9481] "Zbtb37" "Pde7a" "Hps3" "Gyg1"
## [9485] "Cpa3" "Agtr1b" "Naaladl2" "Ect2"
## [9489] "Fndc3b" "Actrt3" "Lrrc31" "Dars2"
## [9493] "4933429H19Rik" "Phc3" "Zmat3" "Kcnmb3"
## [9497] "Gnb4" "Mrpl47" "Pex5l" "Dnajc19"
## [9501] "Dcun1d1" "Mccc1" "Klhl20" "Gm57858"
## [9505] "Qrfpr" "Anxa5" "Ccna2" "Bbs7"
## [9509] "Cetn4" "Nudt6" "Ankrd50" "1700017G19Rik"
## [9513] "Gm16508" "Tex50" "Sclt1" "Ikzf5"
## [9517] "1700018B24Rik" "Slc7a11" "Elf2" "Mgarp"
## [9521] "Maml3" "Frem2" "Ufm1" "Exosc8"
## [9525] "4930558K02Rik" "Ccna1" "Nbea" "Tm4sf1"
## [9529] "Wwtr1" "Commd2" "Gm6394" "Siah2"
## [9533] "P2ry14" "Igsf10" "9330121J05Rik" "Ssr3"
## [9537] "Dnm3" "Gm8388" "E130311K13Rik" "Slc33a1"
## [9541] "Vmn2r-ps11" "4931440P22Rik" "Ccnl1" "Lxn"
## [9545] "Rarres1" "Gm8515" "Snrpd2" "Mettl13"
## [9549] "Gm17641" "Ift80" "Trim59" "Kpna4"
## [9553] "B3galnt1" "Zbbx" "Wdr49" "Golim4"
## [9557] "Gm5277" "Rapgef2" "Prrc2c" "Etfdh"
## [9561] "Tmem144" "Rbm46" "Lrat" "Gm10710"
## [9565] "Tlr2" "Trim2" "Fhdc1" "Prss48"
## [9569] "Kirrel1" "Fmo1" "Ube2l3" "Pear1"
## [9573] "Ntrk1" "Prcc" "Ttc24" "Rhbg"
## [9577] "Bglap" "Slc25a44" "Sema4a" "Lmna"
## [9581] "Fmo2" "Lamtor2" "Rxfp4" "Gm10253"
## [9585] "Dap3" "Rusc1" "Mtx1" "Mir92b"
## [9589] "Trim46" "Slc50a1" "Efna1" "Mroh9"
## [9593] "Efna3" "Efna4" "Adam15" "Zbtb7b"
## [9597] "Flad1" "Cks1b" "4632404H12Rik" "Il6ra"
## [9601] "Gm24046" "Creb3l4" "Prrx1" "Slc27a3"
## [9605] "Npr1" "Gm23464" "Lelp1" "Sprr1b"
## [9609] "Sprr1a" "Sprr4" "Ivl" "Lce1b"
## [9613] "Lce1e" "Gorab" "Lce1g" "Lce1j"
## [9617] "Lce1k" "Crct1" "Lce1m" "G430049J08Rik"
## [9621] "Riiad1" "Tuft1" "Psmb4" "Psmd4"
## [9625] "Blzf1" "Scnm1" "Tnfaip8l2" "Gabpb2"
## [9629] "Mllt11" "Gm128" "6330562C20Rik" "Gm5070"
## [9633] "Adamtsl4" "Ecm1" "Tars2" "Atp1b1"
## [9637] "Prpf3" "Mrps21" "Ciart" "Gm20940"
## [9641] "Plekho1" "Vps45" "Bola1" "H4c14"
## [9645] "Terc" "BC107364" "Huwe1" "Xcl1"
## [9649] "Gm15441" "Polr3gl" "Rpl21-ps11" "Nudt17"
## [9653] "Polr3c" "Gpr89" "Gja8" "Bcl9"
## [9657] "Or13l2" "Pde4dip" "Tbx19" "Phgdh"
## [9661] "Hsd3b3" "Hsd3b6" "Hsd3b1" "Man1a2"
## [9665] "Ttf2" "Ptgfrn" "Cd2" "Vangl1"
## [9669] "Sycp1" "Sft2d2" "Atg4a" "Olfml3"
## [9673] "Dclre1b" "Phtf1os" "Magi3" "Tafa3"
## [9677] "Mov10" "Capza1" "Cttnbp2nl" "Kcnd3os"
## [9681] "Mpzl1" "Rap1a" "Cimap3" "Cept1"
## [9685] "Cd53" "Cym" "Rbm15" "Kcnc4"
## [9689] "Ubl4b" "Strip1" "Csf1" "Pou2f1"
## [9693] "Gstm7" "Gstm6" "Gstm2" "Gstm1"
## [9697] "Gstm4" "Gnai3" "Cyb561d1" "Atxn7l2"
## [9701] "Gm12522" "Celsr2" "5330438I03Rik" "Sars1"
## [9705] "Gpsm2" "Stxbp3" "Fndc7" "Prpf38b"
## [9709] "Eeig2" "Ntng1" "Prmt6" "Gm5548"
## [9713] "Amy1" "Pogk" "Rnpc3" "A930005H10Rik"
## [9717] "Vcam1" "Rtca" "Trmt13" "Mfsd14a"
## [9721] "Slc35a3" "Agl" "1700061I17Rik" "Plppr4"
## [9725] "Uck2" "Snx7" "Rwdd3" "Tlcd4"
## [9729] "Abcd3" "Fnbp1l" "Gm5981" "Usp53"
## [9733] "Mettl14" "Ndst3" "1700006A11Rik" "Gm56171"
## [9737] "1700003H04Rik" "Ugt8a" "Ank2" "Larp7"
## [9741] "Alpk1" "Ap1ar" "Fam241a" "Gm43656"
## [9745] "Egf" "Gar1" "Lrrc52" "Sec24b"
## [9749] "Ostc" "Rpl34" "Gm5982" "Hadh"
## [9753] "Sgms2" "Aimp1" "Gstcd" "Nfkb1"
## [9757] "Cisd2" "Fryl" "Pbx1" "Dapp1"
## [9761] "Mttp" "4930579F01Rik" "2410002F23Rik" "Rap1gds1"
## [9765] "Gm4863" "Gm6214" "Pdha2" "Bmpr1b"
## [9769] "Pdlim5" "Gm5265" "Lmo4" "Hs2st1"
## [9773] "Ccn1" "Dnai3" "Rpf1" "Rpl11"
## [9777] "Adgrl2" "Ifi44l" "Gipc2" "Nexn"
## [9781] "Nuf2" "Miga1" "Msh4" "Rabggtb"
## [9785] "Acadm" "Lhx8" "Cth" "Srsf11"
## [9789] "Tgs1" "Chchd7" "Fam110b" "Uap1"
## [9793] "Ubxn2b" "Sdcbp" "Gm11801" "Chd7"
## [9797] "Clvs1" "Gm12920" "Cfap418" "Gm11829"
## [9801] "Ccne2" "Virma" "Nos1ap" "Rad54b"
## [9805] "Gem" "Rbm12b2" "Gm11841" "Gm6793"
## [9809] "Triqk" "Runx1t1" "Nbn" "Mmp16"
## [9813] "Cngb3" "Atf6" "Ttpa" "Ggh"
## [9817] "Ccnc" "Usp45" "Pnisr" "Coq3"
## [9821] "Faxc" "Mms22l" "Ndufaf4" "Prdx6-ps2"
## [9825] "Dusp12" "Gm11907" "Epha7" "Map3k7"
## [9829] "Bach2" "Casp8ap2" "Mdn1" "Lyrm2"
## [9833] "Gm11942" "Rragd" "Srsf12" "Fcrlb"
## [9837] "Rngtt" "Akirin2" "Rars2" "1700009N14Rik"
## [9841] "Gm12384" "Aco1" "Smim27" "Spink4"
## [9845] "Nfx1" "Nudt2" "Fcrla" "Fam219aos"
## [9849] "Dnai1" "4930578G10Rik" "Phf24" "Spata31g1"
## [9853] "Unc13b" "Atp8b5" "Rusc2" "Creb3"
## [9857] "Rgp1" "Uqcrb" "Npr2" "Serf2"
## [9861] "Tmem8b" "Reck" "Glipr2" "Clta"
## [9865] "Melk" "Zcchc7" "Grhpr" "1700055D18Rik"
## [9869] "G3bp2" "Fcgr2b" "Polr1e" "Frmpd1"
## [9873] "Trmt10b" "Dcaf10" "Stra6l" "Aldh1b1"
## [9877] "Ccdc180" "Tmod1" "Foxe1" "Anp32b"
## [9881] "Fcgr3" "Nans" "Invs" "Msantd3"
## [9885] "Tmeff1" "Cavin4" "Gm12452" "Zfp189"
## [9889] "Rnf20" "Cylc2" "Gm12466" "Sdhc"
## [9893] "Smc2" "Toporsl" "Gm12482" "Or13f5"
## [9897] "Nipsnap3a" "Nipsnap3b" "Slc44a1" "Fsd1l"
## [9901] "Fktn" "Tal2" "Pcp4l1" "Tmem38b"
## [9905] "Zfp462" "Actl7a" "Abitram" "Gm22300"
## [9909] "Pakap" "Zkscan16" "Gng10" "Ugcg"
## [9913] "E130308A19Rik" "Fcer1g" "Snx30" "Slc31a2"
## [9917] "Slc31a1" "Prpf4" "Bspry" "4933430I17Rik"
## [9921] "Rgs3" "Zfp618" "Col27a1" "Mir455"
## [9925] "Ndufs2" "Orm2" "Aknaos" "Tmem268"
## [9929] "Pappa" "Trim32" "Gm11222" "Gm11225"
## [9933] "Kdm4c" "Gm11263" "Snapc3" "Usp21"
## [9937] "Cntln" "Sh3gl2" "Focad" "Ifna5"
## [9941] "Ifna1" "Mtap" "Tgif2-ps1" "Dmrta1"
## [9945] "Gm12643" "Gm12644" "Ufc1" "Gm12653"
## [9949] "Tek" "Fggy" "Hook1" "Nfia"
## [9953] "Patj" "Gm55907" "Atg4c" "Gm10305"
## [9957] "Efcab7" "B930036N10Rik" "Pgm1" "Ube2u"
## [9961] "Raver2" "Dnajc6" "Leprot" "Dynlt5"
## [9965] "Mier1" "Oma1" "Dab1" "Fyb2"
## [9969] "Ly9" "Plpp3" "Gm12727" "Dhcr24"
## [9973] "Fam151a" "Cdcp2" "Ldlrad1" "Ift25"
## [9977] "Ndc1" "Glis1" "Lrp8" "Gm49712"
## [9981] "Slamf7" "Magoh" "Czib" "Slc1a7"
## [9985] "Echdc2" "Orc1" "Kti12" "Rab3b"
## [9989] "Calr4" "Eps15" "Ttc39a" "Gm37065"
## [9993] "Faf1" "Dmrta2" "Bend5" "Trabd2b"
## [9997] "Tal1" "Pdzk1ip1" "Gm12833" "Efcab14"
## [10001] "Mob3c" "Kncn" "Vangl2" "Tmem275"
## [10005] "Pomgnt1" "Gm12950" "Gpbp1l1" "Ccdc163"
## [10009] "Tesk2" "Zswim5" "Hectd3" "Eif2b3"
## [10013] "Ptch2" "Timm23" "Dynlt4" "Gm25099"
## [10017] "Gm23143" "Tmem53" "Hyi" "Med8"
## [10021] "Elovl1" "D4Ertd617e" "Slc2a1" "Svbp"
## [10025] "Pea15a" "Cldn19" "Gm12957" "Hivep3"
## [10029] "Scmh1" "Slfnl1" "Cited4" "Rims3"
## [10033] "Col9a2" "Trit1" "Gm12901" "Casq1"
## [10037] "Rhbdl2" "Mycbp" "Pou3f1" "Fhl3"
## [10041] "Sf3a3" "Mir697" "Inpp5b" "Epha10"
## [10045] "Airim" "Rspo1" "Atp1a2" "Gnl2"
## [10049] "Snip1" "Grik3" "Mrps15" "Oscp1"
## [10053] "Stk40" "Eva1b" "Gm12945" "Clspn"
## [10057] "5730409E04Rik" "Kcnj9" "Psmb2" "Zmym6"
## [10061] "Tmem35b" "Dlgap3" "Csmd2" "A3galt2"
## [10065] "Trim62" "Ak2" "Rnf19b" "Fndc5"
## [10069] "Gm2710" "Yars1" "Sync" "Zbtb8os"
## [10073] "Gm24621" "Bsdc1" "Marcksl1" "Ptp4a2"
## [10077] "Spocd1" "Adgrb2" "Pef1" "Fh1"
## [10081] "Fabp3" "Laptm5" "Mecr" "Srsf4"
## [10085] "Tmem200b" "Gm10300" "Snora16a" "Dnajc8"
## [10089] "Ptafr" "Wasf2" "Cic" "Opn3"
## [10093] "Cd164l2" "Map3k6" "Slc9a1" "Gpatch3"
## [10097] "Ubxn11" "Slc30a2" "Gm5589" "Pafah2"
## [10101] "Paqr7" "Aunip" "Chml" "Rsrp1"
## [10105] "Syf2" "Stpg1" "Il22ra1" "Myom3"
## [10109] "Srsf10" "Fuca1" "Hmgcl" "Gale"
## [10113] "Gm13007" "Rbm8a2" "Tcea3" "Luzp1"
## [10117] "Tex46" "Lactbl1" "Wnt4" "1700013G24Rik"
## [10121] "Hspg2" "Ece1" "Sh2d5" "Kif17"
## [10125] "Cep170" "AB041806" "Mul1" "Camk2n1"
## [10129] "Pla2g2c" "Pla2g2d" "Pla2g2a" "Pla2g2e"
## [10133] "Akr7a5" "Aldh4a1" "Rcc2" "Akt3"
## [10137] "Sdhb" "Mfap2" "Spata21" "Fbxo42"
## [10141] "Arhgef19" "Epha2" "Fam131c" "Hspb7"
## [10145] "Zbtb17" "B330016D10Rik" "Hnrnpu" "AI507597"
## [10149] "Agmat" "Gm13038" "Pramel1" "Pramel12"
## [10153] "Aadacl4fm1" "Gm13127" "Dhrs3" "Zfp985"
## [10157] "Zfp600" "Smyd3" "Zfp991" "Zfp982"
## [10161] "Fv1" "2510039O18Rik" "Mthfr" "Mad2l2"
## [10165] "Mtor" "Exosc10" "Srm" "Casz1"
## [10169] "Coq8a" "Dffa" "Lzic" "Slc2a7"
## [10173] "Eno1" "Rere" "Tnfrsf9" "Gm23405"
## [10177] "Dnajc11" "Hes2" "Rpl22" "Psen2"
## [10181] "Chd5" "Cep104" "Megf6" "B230104I21Rik"
## [10185] "Ttc34" "Mmel1" "Hes5" "Gm10564"
## [10189] "Morn1" "Faap20" "Gm5069" "Cfap74"
## [10193] "Gnb1" "Cdk11b" "Fndc10" "Ssu72"
## [10197] "Mrpl20" "Ccnl2" "Aurkaip1" "Mxra8"
## [10201] "Dvl1" "Gm38164" "Stum" "Ints11"
## [10205] "Acap3" "Sdf4" "Tnfrsf4" "9430015G10Rik"
## [10209] "Rnf223" "Tmem68" "Rps20" "Bpnt2"
## [10213] "Nsmaf" "Mixl1" "Asph" "4930448K20Rik"
## [10217] "Gm11814" "Plekhf2" "Ints8" "Dpy19l4"
## [10221] "Esrp1" "Tmem67" "Cibar1" "Slc26a7"
## [10225] "Ephx1" "Lrrc69" "Otud6b" "Decr1"
## [10229] "Osgin2" "Ripk2" "Cnbd1" "Cpne3"
## [10233] "Wwp1" "Nkain3" "Prdm13" "Ccdc121rt1"
## [10237] "Tstd3" "4930528A17Rik" "Pou3f2" "Klhl32"
## [10241] "Fhl5" "Ufl1" "Gm11895" "Manea"
## [10245] "Pnrc1" "Spaca1" "Lbr" "Orc3"
## [10249] "Gm136" "Smim8" "Mob3b" "C9orf72"
## [10253] "Gm12369" "Gm12387" "Rigi" "Topors"
## [10257] "Ndufb6" "Degs1" "Aptx" "Bag1"
## [10261] "Aqp7" "Aqp3" "Nol6" "Kif24"
## [10265] "Myorg" "Spmip6" "Enho" "Cntfr"
## [10269] "Capn2" "Dctn3" "Sigmar1" "Fancg"
## [10273] "Pigo" "Stoml2" "Atosb" "Rmrp"
## [10277] "Tpm2" "Tln1" "Gba2" "Ccdc185"
## [10281] "Msmp" "Spag8" "Fam221b" "Or13e8"
## [10285] "Or13c7d" "Gne" "Gm56267" "Pax5"
## [10289] "Zbtb5" "Shb" "1700056E22Rik" "Tstd2"
## [10293] "Xpa" "Trmo" "Trim14" "Tbc1d2"
## [10297] "Gm568" "Alg2" "Mrpl50" "Pgap4"
## [10301] "Ppp3r2" "Hlx" "Abca1" "Mexis"
## [10305] "Gm12513" "Actl7b" "Ctnnal1" "Tmem245"
## [10309] "Frrs1l" "Epb41l4b" "Ptpn3" "Gm12526"
## [10313] "Tbl3" "Tmem234" "Mtarc2" "D630039A03Rik"
## [10317] "Txn1" "Or2k2" "Ptgr1" "Shoc1"
## [10321] "Inip" "Gm12542" "Zfp37" "Cdc26"
## [10325] "Wdr31" "C130074G19Rik" "Alad" "Ambp"
## [10329] "Akna" "Tex48" "Tnfsf15" "Hmgb1-rs18"
## [10333] "Gm11224" "Megf9" "Rasef" "Dmac1"
## [10337] "Iars2" "Mpdz" "Nfib" "Zdhhc21"
## [10341] "Frem1" "Ttc39b" "Psip1" "Bnc2"
## [10345] "Haus6" "Plin2" "Mllt3" "9630028B13Rik"
## [10349] "Ifna14" "Mrpl48" "Ifna2" "Gm13274"
## [10353] "Elavl2" "Gm12669" "Izumo3" "Gm12642"
## [10357] "Tusc1" "Gm23443" "Gm9722" "Caap1"
## [10361] "Plaa" "Eqtn" "Mysm1" "Jun"
## [10365] "Gm12695" "Gm12696" "Tm2d1" "Itgb3bp"
## [10369] "Ccdc50-ps" "Lyplal1" "Jak1" "Gm12799"
## [10373] "Insl5" "4921539E11Rik" "Prkaa2" "Gm12722"
## [10377] "Pcsk9" "Cimap2" "Ttc4" "Mroh7"
## [10381] "Rrp15" "Tceanc2" "Lrrc42" "Lrp8os1"
## [10385] "Cpt2" "Podn" "Scp2" "Zyg11b"
## [10389] "Shisal2a" "Prpf38a" "Rnf11" "Kctd3"
## [10393] "4930522H14Rik" "Cdkn2c" "Gm55392" "Rpl3"
## [10397] "Foxe3" "Cmpk1" "Dmbx1" "Nsun4"
## [10401] "Uqcrh" "Lurap1" "Kcnk2" "Tspan1"
## [10405] "Llph" "Tmem69" "Mmachc" "Toe1"
## [10409] "Hpdl" "Dmap1" "Klf17" "Dph2"
## [10413] "Artn" "Cenpf" "St3gal3" "Kdm4a"
## [10417] "Szt2" "Cdc20" "Mpl" "Ccnb1"
## [10421] "Gm12865" "Zfp691" "Ermap" "Tmem269"
## [10425] "Wars1" "Smyd2" "AU022252" "Ccdc30"
## [10429] "Ppcs" "Guca2b" "Ctps1" "Mir30c-1"
## [10433] "Exo5" "Zfp69" "Smap2" "Zmpste24"
## [10437] "Vash2" "Tmco2" "Rlf" "Gm12877"
## [10441] "Cap1" "Gm17244" "Ppie" "Oxct2a"
## [10445] "Ndufs5" "Akirin1" "D130007C19Rik" "Flvcr1"
## [10449] "Utp11" "Cdca8" "Dnali1" "Sh3d21"
## [10453] "Map7d1" "Tekt2" "Ago3" "Ago1"
## [10457] "Tfap2e" "Rps28" "Tatdn3" "Gja4"
## [10461] "Gjb3" "CK137956" "Hmgb4" "Zscan20"
## [10465] "Zfp362" "Hpca" "S100pbp" "Nhsl3"
## [10469] "Rbbp4" "Garin4" "Hdac1" "Lck"
## [10473] "Fam167b" "Eif3i" "Iqcc" "Txlna"
## [10477] "Tmem39b" "Khdrbs1" "Tinagl1" "Ldc1"
## [10481] "Nenf" "Serinc2" "Gm10570" "Zcchc17"
## [10485] "Epb41" "Oprd1" "Gmeb1" "Trnau1ap"
## [10489] "Rcc1" "Snora73b" "Snora73a" "1700034H15Rik"
## [10493] "Phactr4" "Med18" "Sesn2" "Atp5if1"
## [10497] "Xkr8" "Smpdl3b" "Themis2" "Stx12"
## [10501] "Fam76a" "Gpr3" "Traf5" "Tmem222"
## [10505] "Trnp1" "Nudc" "Gm25270" "Rps6ka1"
## [10509] "Dhdds" "Lin28a" "Sh3bgrl3" "Cep85"
## [10513] "Catsper4" "Hhat" "Zfp593" "Fam110d"
## [10517] "Extl1" "Man1c1" "Tmem50a" "Srrm1"
## [10521] "Gm12990" "Nipal3" "Grhl3" "Pnrc2"
## [10525] "Sertad4" "Lypla2" "Pithd1" "Eloa"
## [10529] "C1qb" "C1qc" "C1qa" "Cdc42"
## [10533] "Alpl" "Pink1" "Cda" "Anapc2"
## [10537] "Syt14" "Vwa5b1" "Pla2g2f" "Pla2g5"
## [10541] "Otud3" "Gm16287" "Mrto4" "Igsf21"
## [10545] "Gm9867" "Arhgef10l" "Padi6" "G0s2"
## [10549] "Padi3" "Crocc" "Necap2" "Clcnka"
## [10553] "Clcnkb" "Spen" "Tmem82" "Slc25a34"
## [10557] "Plekhm2" "Dnajc16" "Cr1l" "Cela2a"
## [10561] "Ctrc" "Fhad1" "Kazn" "Prdm2"
## [10565] "Gm13042" "Trappc2" "Pramel5" "Pramel13"
## [10569] "Cfap107" "Cnksr3" "Tnfrsf1b" "Tnfrsf8"
## [10573] "Gm13229" "Rps19-ps3" "Zfp933" "Miip"
## [10577] "Plod1" "Clcn6" "Agtrap" "Fbxo6"
## [10581] "Syne1" "Fbxo44" "Disp3" "Ubiad1"
## [10585] "Angptl7" "Tardbp" "Cort" "Rpsa-ps12"
## [10589] "Pgd" "Kif1b" "Rbp7" "Zbtb2"
## [10593] "Nmnat1" "Slc25a33" "Spsb1" "H6pd"
## [10597] "Car6" "Gm13092" "Vamp3" "Phf13"
## [10601] "Gm9768" "Zbtb48" "Lrp11" "Espn"
## [10605] "Hes3" "Rnf207" "Ajap1" "BC049688"
## [10609] "Smim1" "Ccdc27" "Trp73" "5930403L14Rik"
## [10613] "Actrt2" "Nup43" "Prxl2b" "Tnfrsf14"
## [10617] "Plch2" "Rer1" "Prkcz" "Gm13171"
## [10621] "1500002C15Rik" "Atad3a" "Tmem88b" "Mxra8os"
## [10625] "Katna1" "Tas1r3" "Cptp" "Gm16008"
## [10629] "Ttll10" "Agrn" "Cdk6" "Fam133b"
## [10633] "1700109H08Rik" "Akap9" "Gm38697" "Ppil4"
## [10637] "Tex47" "Gm8802" "Steap4" "Sri"
## [10641] "Abcb1a" "Abcb4" "Tmem243" "Elapor2"
## [10645] "Gm6641" "Speer3" "Ddx24" "Gm25682"
## [10649] "Sema3e" "Pclo" "Cacna2d1" "Speer4f1"
## [10653] "Sema3c" "Magi2" "Tmem60" "Fgl2"
## [10657] "Fam185a" "Armc10" "Gm23680" "Pmpcb"
## [10661] "Psmc2" "Kmt2e" "Gm9836" "Nos3"
## [10665] "Abcb8" "Agap3" "1700022A21Rik" "Nub1"
## [10669] "1500035N22Rik" "Sf3b5" "Dpp6" "Rbm33"
## [10673] "Nom1" "Dnajb6" "Selenoi" "Drc1"
## [10677] "Cimip2c" "Kcnk3" "Slc35f6" "Cenpa"
## [10681] "Plagl1" "Dpysl5" "Emilin1" "Abhd1"
## [10685] "Tcf23" "Atraid" "Dnajc5g" "Trim54"
## [10689] "Snx17" "Nrbp1" "Krtcap3" "Fuca2"
## [10693] "Zfp512" "Ccdc121" "Gpn1" "Slc4a1ap"
## [10697] "Mrpl33" "Babam2" "Fosl2" "Plb1"
## [10701] "Ppp1cb" "Ywhah" "Adat2" "Maea"
## [10705] "Uvssa" "Gm10459" "Rps29" "Nsd2"
## [10709] "Nicol1" "Rnf4" "Fam193a" "Sh3bp2"
## [10713] "Add1" "Nmbr" "Grk4" "Htt"
## [10717] "Msantd1" "Rgs12" "Adra2c" "Hmx1"
## [10721] "Plk-ps1" "Ablim2" "Afap1" "Grpel1"
## [10725] "Cited2" "Jakmip1" "Gm1043" "Crmp1"
## [10729] "Evc2" "Cytl1" "Stx18" "Tmem128"
## [10733] "Otop1" "Drd5" "Dnaja1" "Txlnb"
## [10737] "Cir1" "Gm16401" "Gm42984" "4930431F12Rik"
## [10741] "Lap3" "Slit2" "Gm40319" "Sod3"
## [10745] "Anapc4" "Smim20" "Gm10827" "Tbc1d19"
## [10749] "Stim2" "Pcdh7" "Gm6632" "G6pd2"
## [10753] "Nwd2" "Pgcka1" "Klf3" "Fam114a1"
## [10757] "Klhl5" "Rab14" "Nhsl1" "Klb"
## [10761] "Lias" "Uchl1" "Limch1" "Gm6517"
## [10765] "Tmem33" "Slc30a9" "C330024D21Rik" "Gm5867"
## [10769] "Guf1" "Tpi-rs5" "Atp10d" "Ociad1"
## [10773] "Gm34583" "Rasl11b" "Pdgfra" "Kit"
## [10777] "Srd5a3" "Gm7467" "Cep135" "Cracd"
## [10781] "Ifngr1" "Paics" "Arl9" "Rest"
## [10785] "Adgrl3" "Hmgn2" "Csn1s1" "Gm7337"
## [10789] "BC051076" "Cabs1" "Gm7721" "Il20ra"
## [10793] "Utp3" "Rufy3" "Mob1b" "Dck"
## [10797] "Gm9958" "Pf4" "Cxcl3" "Cxcl1"
## [10801] "Mthfd2l" "Areg" "Map3k5" "Parm1"
## [10805] "Thap6" "Uso1" "Art3" "Fam47e"
## [10809] "Shroom3" "Gm6450" "Gm22915" "Septin11"
## [10813] "Ccng2" "Rpl32l" "Gm25937" "Cxcl13"
## [10817] "Mrpl1" "Anxa3" "Bmp2k" "Gm8048"
## [10821] "Fgf5" "Bmp3" "Gm16226" "Enoph1"
## [10825] "Mtfr2" "Cops4" "Mrps18c" "Gpat3"
## [10829] "Arhgap24" "Ptpn13" "Aff1" "Nudt9"
## [10833] "Dmp1" "Thoc2l" "Lrrc8c" "Gm2467"
## [10837] "Zfp326" "Cdc7" "n-R5s173" "Btbd8"
## [10841] "Rpap2" "Mtf2" "Ccdc18" "Pigg"
## [10845] "Pcgf3" "Idua" "Aldh8a1" "Fgfrl1"
## [10849] "Plcxd1" "Golga3" "Gm42596" "Ddx51"
## [10853] "Ttc28" "Pitpnb" "Crybb1" "Tfip11"
## [10857] "Hps4" "1700021A07Rik" "Ccdc121rt2" "Aym1"
## [10861] "Wscd2" "Usp30" "Ung" "Acacb"
## [10865] "Ube3b" "Fam222a" "Tchp" "4930519G04Rik"
## [10869] "Pabpn1" "1700020N01Rik" "Oasl2" "Oasl1"
## [10873] "2210016L21Rik" "Sppl3" "Coq5" "Srsf9"
## [10877] "Triap1" "Msi1" "Pla2g1b" "Pxn"
## [10881] "Sgk1" "Rplp0" "Gcn1" "Rab35"
## [10885] "Cit" "Taok3" "Vsig10" "Wsb2"
## [10889] "Gm9754" "Hrk" "Tbx5" "Gm10825"
## [10893] "Rbm19" "Slc8b1" "Iqcd" "Ddx54"
## [10897] "Rasal1" "Hectd4" "Brap" "Atxn2"
## [10901] "Pptc7" "Vps29" "Slc2a12" "Gpn3"
## [10905] "Arpc3" "Anapc7" "P2rx4" "A930024E05Rik"
## [10909] "Tmem120b" "Gm38102" "Setd1b" "Cfap251"
## [10913] "Mlxip" "Gm37416" "Lrrc43" "Kntc1"
## [10917] "Denr" "Ccdc62" "Hip1r" "Arl6ip4"
## [10921] "Kmt5a" "Snrnp35" "Tmed2" "Ddx55"
## [10925] "Slc18b1" "Gtf2h3" "Atp6v0a2" "Dnah10"
## [10929] "Zfp664" "Rflna" "Gm10382" "Bri3bp"
## [10933] "Aacs" "Tmem132b" "Tmem132c" "Taar7b"
## [10937] "Glt1d1" "Fzd10" "Ran" "Adgrd1"
## [10941] "Sfswap" "Mmp17" "Mrps17" "Nipsnap2"
## [10945] "Cct6a" "Zbed5" "Stx7" "Nupr2"
## [10949] "Crcp" "Tpst1" "Kctd7" "Tyw1"
## [10953] "Gtf2ird2" "Rfc2" "Gm10369" "Mettl27"
## [10957] "Cldn3" "Ccn2" "Abhd11" "Stx1a"
## [10961] "Dnajc30" "Mlxipl" "Tbl2" "Bcl7b"
## [10965] "Nsun5" "Rhbdd2" "Por" "Srrm3"
## [10969] "Gm4777" "Hspb1" "Dtx2" "Upk3b"
## [10973] "Upk3bl" "Rasa4" "Polr2j" "Alkbh4"
## [10977] "Myl10" "Fis1" "Cldn15" "Nmt1"
## [10981] "Epb41l2" "Plod3" "Actl6b" "Lrch4"
## [10985] "Tsc22d4" "Ppp1r35" "Zcwpw1" "Smok3c"
## [10989] "Zkscan1" "Zscan21" "Cops6" "Arhgap18"
## [10993] "Ap4m1" "Cnpy4" "Mblac1" "Lamtor4"
## [10997] "Pvrig" "Gm10874" "Zfp157" "A430033K04Rik"
## [11001] "Fam20c" "Foxl3" "Ptprk" "6330403L08Rik"
## [11005] "Dnaaf5" "Sun1" "Get4" "Gper1"
## [11009] "Mafk" "Elfn1" "Nudt1" "Eif3b"
## [11013] "Amz1" "Pebp1" "Gm26970" "Foxk1"
## [11017] "Wipi2" "Slc29a4" "Spdye4b" "Zfp12"
## [11021] "Daglb" "Fam220a" "Cyth3" "Pms2"
## [11025] "Mtcl3" "Bhlha15" "Bri3" "Nptx2"
## [11029] "Trrap" "1700018F24Rik" "Arpc1b" "Bud31"
## [11033] "Cpsf4" "Zkscan5" "Zscan25" "Echdc1"
## [11037] "Cdk8" "Wasf3" "Gtf3a" "Polr1d"
## [11041] "Gsx1" "Pdx1" "Gm6054" "Pomp"
## [11045] "Mtus2" "Alox5ap" "Hddc2" "Tex26"
## [11049] "Wdr95" "Fry" "Brca2" "Rbm48"
## [11053] "Gatad1" "Fzd1" "Cdk14" "Cldn12"
## [11057] "Steap2" "Trdn" "Steap1" "Gm5714"
## [11061] "Gm24525" "Adam22" "Rundc3b" "Crot"
## [11065] "Dmtf1" "4930568A13Rik" "Cd36" "Gnai1"
## [11069] "Tspyl1" "Rsbn1l" "Ptpn12" "Rpl31-ps21"
## [11073] "Ccdc146" "Fbxl13" "Napepld" "Dnajc2"
## [11077] "Reln" "Orc5" "Gm15421" "Tspyl4"
## [11081] "5031425E22Rik" "Tomm7" "Gabarapl2" "Kcnh2"
## [11085] "Atg9b" "Cdk5" "Tmub1" "Asb10"
## [11089] "Iqca1l" "Smarcd3" "Rps27" "Gstm3"
## [11093] "Rheb" "E130116L18Rik" "Kmt2c" "Gm10062"
## [11097] "Xrcc2" "Speer4a1" "4930584F24Rik" "Speer4b"
## [11101] "Shh" "Lmbr1" "Hdac2" "Cib4"
## [11105] "Gm9899" "Ost4" "Cgref1" "Slc5a6"
## [11109] "Ucn" "Mpv17" "Eif2b4" "Gm9970"
## [11113] "Ift172" "Lama4" "Gm40275" "Rbks"
## [11117] "Gm10461" "Prr14l" "Nkx1-1" "G630022F23Rik"
## [11121] "Letm1" "Haus3" "Tnip2" "Mfsd10"
## [11125] "Tube1" "Nop14" "Lrpap1" "Cpz"
## [11129] "Trmt44" "4931431C16Rik" "Htra3" "2210406O10Rik"
## [11133] "Tbc1d14" "D5Ertd579e" "Bloc1s4" "Fyn"
## [11137] "Man2b2" "Stk32b" "Zbtb49" "Slc2a9"
## [11141] "Wdr1" "Zfp518b" "Gm43806" "Rab28"
## [11145] "Nkx3-2" "Bod1l" "Gm8055" "Gm5298"
## [11149] "Gm7181" "Gm5554" "Gm7854" "Prom1"
## [11153] "Tapt1" "D5Ertd615e" "Qdpr" "Fam184b"
## [11157] "Lcorl" "Mettl24" "Kcnip4" "Ccdc149"
## [11161] "8030423F21Rik" "Arap2" "Nwd2os" "Rell1"
## [11165] "Gm43840" "Gm20033" "Tmem156" "Ugdh"
## [11169] "Wasf1" "Smim14" "Rbm47" "Gm15794"
## [11173] "Atp8a1" "Kctd8" "Gnpda2" "Cox7b2"
## [11177] "Commd8" "Corin" "Nfxl1" "Ak9"
## [11181] "Zar1" "Txk" "Gm9870" "Slain2"
## [11185] "Lrrc66" "Chic2" "Clock" "Pdcl2"
## [11189] "A730089K16Rik" "Aasdh" "Mical1" "Ppat"
## [11193] "Noa1" "Igfbp7" "Pea15b-ps" "Cenpc1"
## [11197] "Uba6" "Tmprss11c" "Sult1e1" "Csn2"
## [11201] "Grsf1" "Naa60" "Sesn1" "Mkrn1-ps1"
## [11205] "Gc" "Adamts3" "Rchy1" "Cdkl2"
## [11209] "Ppef2" "Naaa" "Cxcl11" "Nup54"
## [11213] "Scarb2" "Snx3" "Ccdc158" "Paqr3"
## [11217] "Gk2" "Antxr2" "A730035I17Rik" "1700010H22Rik"
## [11221] "Rasgef1b" "Hnrnpd" "Hnrnpdl" "Tmem150c"
## [11225] "Ostm1" "Gm8091" "Gm19620" "Plac8"
## [11229] "Coq2" "Hpse" "Abraxas1" "Nkx6-1"
## [11233] "Wdfy3" "Mapk10" "Klhl8" "Sec63"
## [11237] "Hsd17b11" "Sparcl1" "Zfp951" "Gbp8"
## [11241] "Gbp4" "Rps15a" "Gm19566" "Barhl2"
## [11245] "Hfm1" "Tgfbr3" "Bend3" "Gfi1"
## [11249] "Evi5" "Dipk1a" "Tmed5" "Atp5me"
## [11253] "Slc49a3" "Cplx1" "Gak" "Rnf212"
## [11257] "Gm8508" "Cd24a" "AB010352" "Gtpbp6"
## [11261] "5930411N13Rik" "Pgam5" "Pxmp2" "P2rx2"
## [11265] "Fbrsl1" "Noc4l" "Gm22716" "Pus1"
## [11269] "F930017D23Rik" "Ulk1" "Hscb" "E130006D01Rik"
## [11273] "Srrd" "Ccdc121rt3" "Sez6l" "Myo18b"
## [11277] "Grk3" "Crybb2" "Crybb3" "Gm9034"
## [11281] "2900026A02Rik" "F830115B05Rik" "Cmklr1" "Sart3"
## [11285] "Selplg" "Coro1c" "Ssh1" "Alkbh2"
## [11289] "Foxn4" "Kctd10" "Rtn4ip1" "Trpv4"
## [11293] "Gltp" "Git2" "4930515G01Rik" "2610524H06Rik"
## [11297] "Ywhaq-ps2" "Hnf1a" "Acads" "Unc119b"
## [11301] "Mlec" "Gm5950" "Gatc" "Cox6a1"
## [11305] "4930430O22Rik" "Sirt4" "1110006O24Rik" "Bicdl1"
## [11309] "Ccdc60" "Srrm4" "Suds3" "Gm10399"
## [11313] "Hp1bp3" "Gm6983" "Rfc5" "Fbxw8"
## [11317] "Rnft2" "Sdsl" "Plbd2" "Gm43579"
## [11321] "Dtx1" "Rph3a" "Ptpn11" "Trafd1"
## [11325] "Prep" "Erp29" "Adam1b" "Adam1a"
## [11329] "Mapkapk5" "Aldh2" "Acad10" "Cux2"
## [11333] "Ccdc63" "Tctn1" "Rad9b" "Popdc3"
## [11337] "Gm10064" "Anapc5" "Kdm2b" "Morn3"
## [11341] "Il31" "Diablo" "Clip1" "Zcchc8"
## [11345] "Rsrc2" "Vps37b" "Popdc1" "Abcb9"
## [11349] "Pitpnm2" "Rilpl1" "Eif2b1" "Ccdc92"
## [11353] "Ncor2" "Scarb1" "Dhx37" "Gm7774"
## [11357] "Slc15a4" "Vgll2" "Fzd10os" "Rimbp2"
## [11361] "Stx2" "Septin14" "Gusb" "Asl"
## [11365] "Sbds" "A330070K13Rik" "Galnt17" "Auts2"
## [11369] "Dcbld1" "Ncf1" "Gtf2ird1" "Clip2"
## [11373] "Lat2" "Eif4h" "Eln" "Tmem270"
## [11377] "Cldn13" "Cldn4" "Wbscr25" "Nus1"
## [11381] "Vps37d" "Fzd9" "Pom121" "Hip1"
## [11385] "Tmem120a" "Styxl1" "Ssc4d" "Gm56207"
## [11389] "Lrwd1" "Prkrip1" "Pln" "Gm5050"
## [11393] "Cux1" "Znhit1" "Ap1s1" "Serpine1"
## [11397] "Trim56" "Slc12a9" "Zan" "Mospd3"
## [11401] "Pcolce" "Tmem229b" "Agfg2" "Zfp113"
## [11405] "Mir25" "Mir93" "Taf6" "Trappc14"
## [11409] "Gpc2" "1700123K08Rik" "Zfp68" "Pdgfa"
## [11413] "Asf1a" "Adap1" "Chlsn" "4930432F04Rik"
## [11417] "Zfand2a" "Ints1" "Tmem184a" "Psmg3"
## [11421] "Mad1l1" "Snx8" "Grifin" "Rnf220"
## [11425] "Dpm2" "Msl3l2" "Ttyh3" "Iqce"
## [11429] "Gna12" "Card11" "Papolb" "Mmd2"
## [11433] "Tnrc18" "Gm15770" "Or10ah1-ps1" "Gm7291"
## [11437] "Smpdl3a" "Rbakdn" "Rbak" "Spdye4a"
## [11441] "Ints15" "Rac1" "Ankrd61" "Ccz1"
## [11445] "Tecpr1" "Baiap2l1" "Tmem130" "Gcc2"
## [11449] "Gm4871" "Pdap1" "Ptcd1" "Atp5mf"
## [11453] "Zkscan14" "1700001J03Rik" "Rnf6" "Usp12"
## [11457] "Mtif3" "Lnx2" "Ccdc138" "Flt3"
## [11461] "Flt1" "Slc46a3" "Gm10167" "Slc7a1"
## [11465] "Katnal1" "Hmgb1" "Zar1l" "N4bp2l2"
## [11469] "Stard13" "Sh3rf3" "Rfc3" "Zfp788"
## [11473] "Vmn2r-ps54" "Gm2651" "Vps50" "Col1a2"
## [11477] "Casd1" "Ppp1r9a" "Asb4" "Dync1i1"
## [11481] "Sowahc" "Dlx6" "Sdhaf3" "Tac1"
## [11485] "C1galt1" "Mios" "Nxph1" "Phf14"
## [11489] "Gm54938" "Hormad1" "Tmem106b" "P4ha1"
## [11493] "Foxp2" "Tes" "Cav1" "Capza2"
## [11497] "St7" "Cftr" "Lsm8" "Ankrd7"
## [11501] "Cped1" "Wnt16" "Gm10322" "Asb15"
## [11505] "Lmod2" "Spam1" "6530409C15Rik" "Snd1"
## [11509] "Mir129-1" "Hilpda" "Calu" "Ccdc136"
## [11513] "Flnc" "Micu1" "Irf5" "Tspan33"
## [11517] "Smo" "Smkr-ps" "Nrf1" "Cpa1"
## [11521] "Mest" "Mir335" "Mkln1" "1700012A03Rik"
## [11525] "Ascc1" "Akr1b8" "Akr1b10" "Akr1b7"
## [11529] "Bpgm" "Cald1" "Agbl3" "Stra8"
## [11533] "Akr1d1" "Atp6v0c" "Tmem213" "Golm1"
## [11537] "Spock2" "Gm7504" "Ift56" "Luc7l2"
## [11541] "Clec2l" "Tbxas1" "4930599N23Rik" "Ndufb2"
## [11545] "Tmem178b" "Prss2" "Try4" "Vsir"
## [11549] "Try10" "Prss1l" "Gm5409" "Ephb6"
## [11553] "Llcfc1" "Gstk1" "Casp2" "Zyx"
## [11557] "Or2a25" "Or2a7" "Prf1" "Rny3"
## [11561] "Zfp282" "Zfp956" "Krba1" "Sspo"
## [11565] "Atp6v0e2" "Lrrc61" "Repin1" "Zfp775"
## [11569] "Gimap4" "Nodal" "Gimap1" "Tmem176a"
## [11573] "Aoc1" "Aoc1l2" "Aoc1l1" "Malsu1"
## [11577] "Fam221a" "Npy" "Pals2" "Gm56926"
## [11581] "Lrrc20" "Nfe2l3" "Evx1" "Tax1bp1"
## [11585] "Prr15" "Plekha8" "Gars1" "Mindy4"
## [11589] "Ghrhr" "Adcyap1r1" "Avl9" "Ppa1"
## [11593] "Fkbp9" "4930533I22Rik" "Gm20673" "Abcg2"
## [11597] "Tigd2" "Ccser1" "Tnip3" "4930544G11Rik"
## [11601] "Mad2l1" "Gm15644" "Tysnd1" "Serbp1"
## [11605] "Igkv2-137" "Eif2ak3" "Gm1070" "Cd8b1"
## [11609] "Cd8a" "Rnf103" "Chmp3" "Immt"
## [11613] "Polr1a" "Aifm2" "0610030E20Rik" "Tmem150a"
## [11617] "Ggcx" "Capg" "Retsat" "Gm15401"
## [11621] "Suclg1" "Gm6261" "Gcfc2" "Eva1a"
## [11625] "4930507D05Rik" "Gm31861" "M1ap" "Pcgf1"
## [11629] "1700003E16Rik" "Dctn1" "Mob1a" "Bola3"
## [11633] "B230319C09Rik" "Vax2" "Atp6v1b1" "4933428P19Rik"
## [11637] "Ankrd53" "Nagk" "Rpl18" "Dysf"
## [11641] "Npm3-ps1" "Emx1" "Smyd5" "Tprkb"
## [11645] "Figla" "Tgfa" "Ankrd17" "Slc25a16"
## [11649] "Snrpg" "Tia1" "Asprv1" "Aak1"
## [11653] "Nfu1" "Efcc1" "Gp9" "Hmces"
## [11657] "Gm5577" "Gata2" "Dna2" "Dnajb8"
## [11661] "Ruvbl1" "Mgll" "Gm15612" "Tpra1"
## [11665] "4933427D06Rik" "Gm1965" "Vmn1r40" "BC048671"
## [11669] "Uroc1" "Pbld2" "Klf15" "Aldh1l1"
## [11673] "Hdac11" "Fbln2" "Tmem43" "Lsm3"
## [11677] "Slc6a6" "Ccdc174" "Fgd5" "Nr2c2"
## [11681] "Atoh7" "Slc25a26" "Kbtbd8" "Arl6ip5"
## [11685] "Gpr27" "Btf3-ps6" "Gxylt2" "Ppp4r2"
## [11689] "Cntn6" "Trnt1" "Setmar" "Dnajc12"
## [11693] "Edem1" "Gm15519" "Thumpd3" "Mtmr14"
## [11697] "Brpf1" "Ogg1" "Ttll3" "Jagn1"
## [11701] "Il17re" "Il17rc" "Jmjd1c" "Creld1"
## [11705] "Fancd2" "Brk1" "Irak2" "Slc6a11"
## [11709] "Slc6a1" "Hrh1" "Atg7" "Pparg"
## [11713] "D830050J10Rik" "Egr2" "Rho" "H2az1"
## [11717] "Zfand4" "Or6d12" "Or6d13" "Or6d14"
## [11721] "Cxcl12" "Zfp637" "Zfp239" "Gm4875"
## [11725] "Rhobtb1" "Dcp1b" "Cacna2d4" "Fbxl14"
## [11729] "Gm15532" "Tuba8" "A2m" "1700063H04Rik"
## [11733] "Nanog" "Foxj2" "Necap1" "Ank3"
## [11737] "C1rl" "C1ra" "Cdca3" "Pianp"
## [11741] "Zfp384" "Ing4" "Acrbp" "Lpar5"
## [11745] "Chd4" "Nop2" "Ccdc6" "Iffo1"
## [11749] "Mrpl51" "Vamp1" "Scnn1a" "Tnfrsf1a"
## [11753] "Ano2" "D6Wsu163e" "Gm43124" "Fgf23"
## [11757] "Gm4968" "Mtif2" "Mrln" "Parp11"
## [11761] "Cracr2a" "Tspan11" "Nrip2" "Gm10069"
## [11765] "Clec2h" "Clec2d" "Gabarapl1" "Mir680-1"
## [11769] "Prp2" "Slc16a9" "Smim10l1" "Gm34149"
## [11773] "Etv6" "Bcl2l14" "Borcs5" "Cdkn1b"
## [11777] "Apold1" "Ddx47" "Fam234b" "Gm15476"
## [11781] "Fam13c" "Gm55605" "Atf7ip" "BC049715"
## [11785] "Pde6h" "Ptpro" "Dera" "Mgst1"
## [11789] "Pyroxd1" "Golt1b" "Cmas" "4930533K18Rik"
## [11793] "Gm7457" "D6Ertd474e" "Etfrf1" "1700073E17Rik"
## [11797] "Rassf8" "Sspn" "Fgfr1op2" "Med21"
## [11801] "Stk38l" "Gm6266" "Etv5" "Bmal2"
## [11805] "Ppfibp1" "Rep15" "Mrps35" "Ccdc91"
## [11809] "Far2" "Rps4l" "Etfbkmt" "Nacc1"
## [11813] "Bicd1" "Zwint" "Samd9l" "Calcr"
## [11817] "Tfpi2" "Bet1" "Sgce" "Gmfg"
## [11821] "Pon3" "Pon2" "Pdk4" "Rps27a"
## [11825] "Pcdh15" "Sem1" "Rnps1" "Gm16042"
## [11829] "Thsd7a" "Tmem168" "Samtor" "Asz1"
## [11833] "Cttnbp2" "Tspan12" "Fam3c" "Gm5778"
## [11837] "Aass" "Fezf1" "Rnf148" "Iqub"
## [11841] "Ndufa5" "Gm5302" "Gpr37" "Pot1a"
## [11845] "Zfp800" "Gcc1" "Rab36" "Lrrc4"
## [11849] "Rbm28" "Impdh1" "Kcp" "1700080G18Rik"
## [11853] "Gm55823" "Zc3hc1" "Cep41" "Tsga13"
## [11857] "Klf14" "Bcr" "Lncpint" "Plxna4"
## [11861] "Chchd3" "Npn2" "Wdr91" "Cnot4"
## [11865] "Slc13a4" "9330158H04Rik" "Ybx1" "Zc3hav1l"
## [11869] "Copa" "Specc1l" "Zc3hav1" "Hipk2"
## [11873] "Kdm7a" "Slc37a3" "Mrps33" "Dennd11"
## [11877] "Try5" "Prss3" "Fam131b" "Epha1"
## [11881] "Gm5779" "Or2r11" "Tcaf1" "Tpk1"
## [11885] "Ezh2" "Rny1" "Pdia4" "Rpl35a"
## [11889] "Zfp777" "Zfp746" "Rarres2" "Ggt5"
## [11893] "Tmem176b" "Tra2a" "Npvf" "Gm32479"
## [11897] "Hnrnpa2b1" "Skap2" "Hoxa4" "Hoxa5"
## [11901] "Hoxa6" "Hoxa7" "Gm19326" "Hoxa9"
## [11905] "Mir196b" "Jazf1" "Cpvl" "Scrn1"
## [11909] "Fkbp14" "Ggct" "Crhr2" "Lsm5"
## [11913] "Kbtbd2" "Derl3" "Nt5c3" "Ppm1k"
## [11917] "Gprin3" "Gm22622" "Gm22723" "Snca"
## [11921] "Mageb16" "Gadd45a" "Igkv4-86" "Rprl1"
## [11925] "Chchd10" "Spmip9" "Thnsl2" "Gm38828"
## [11929] "Rmnd5a" "Mrpl35" "Ptcd3" "Atoh8"
## [11933] "Vamp8" "Sh2d6" "Elmod3" "Vpreb3"
## [11937] "Tcf7l1" "Kcmf1" "Tmsb10" "Gm24533"
## [11941] "Dnah6" "Gm9001" "Ctnna2" "Mrpl19"
## [11945] "Hk2" "Tlx2" "Gm5134" "Wbp1"
## [11949] "Wdr54" "Mthfd2" "Tet3" "Dguok"
## [11953] "Actg2" "Stambp" "Clec4f" "Tex261"
## [11957] "Gm7443" "Zfp280b" "Paip2b" "Gm10445"
## [11961] "Gm5878" "Spr" "Rab11fip5" "Pradc1"
## [11965] "Fbxo41" "Egr4" "Nat8f5" "Nat8"
## [11969] "S100b" "Nat8f4" "Dusp11" "Pcyox1"
## [11973] "Pcbp1" "Mxd1" "Gkn1" "Aplf"
## [11977] "Cfap92" "Isy1" "Rps19-ps9" "Zkscan3"
## [11981] "Gm9744" "H1f10" "1700031F10Rik" "Eefsec"
## [11985] "Sec61a1" "Abtb1" "Podxl2" "Plxna1"
## [11989] "Vmn1r-ps25" "Vmn1r43" "Chst13" "2610028H24Rik"
## [11993] "Cfap100" "Iqsec1" "Nup210" "Wnt7a"
## [11997] "Chchd4" "Grip2" "Mrps25" "Rbsn"
## [12001] "Trh" "Prickle2" "Lss" "Adamts9"
## [12005] "Magi1" "Nup50l" "Tafa4" "Eogt"
## [12009] "Tmf1" "Uba3" "Frmd4b" "Gm25852"
## [12013] "Gm23510" "Spatc1l" "Foxp1" "Eif4e3"
## [12017] "Prok2" "Rybp" "Ddx3x" "Sumf1"
## [12021] "5031434C07Rik" "Ssu2" "Oxtr" "Rad18"
## [12025] "Ftcd" "Srgap3" "Lhfpl4" "Camk1"
## [12029] "Tada3" "Rpusd3" "Fancd2os" "Ghrl"
## [12033] "Sec13" "Atp2b2" "Vgll4" "Gm10787"
## [12037] "Tamm41" "Raf1" "Gm14335" "Snora7a"
## [12041] "Efcab12" "Mbd4" "Plxnd1" "Or6d15"
## [12045] "Zfp422" "Rassf4" "Slc19a1" "Tmem72"
## [12049] "Rpl28-ps4" "4933440N22Rik" "Fxyd4" "Csgalnact2"
## [12053] "Ret" "Bms1" "Zfp248" "Ankrd26"
## [12057] "Lrtm2" "Pofut2" "Wnt5b" "Erc1"
## [12061] "Wnk1" "Ccdc77" "Tmem121b" "Hdhd5"
## [12065] "Atp6v1e1" "Mical3" "Phc1" "C3ar1"
## [12069] "Ube2g2" "1700013D24Rik" "Pex5" "Emg1"
## [12073] "Mir200c" "Ptpn6" "Grcc10" "Atn1"
## [12077] "Tpi1" "Usp5" "Gnb3" "Krtap12-23"
## [12081] "Gpr162" "Lag3" "Cops7a" "Ncapd2"
## [12085] "Tapbpl" "Tuba3a" "Ltbr" "Cd9"
## [12089] "Ndufa9" "Rad51ap1" "Sec22b" "Krtap12-21"
## [12093] "Tigar" "Ccnd2" "Gm7308" "Gm55163"
## [12097] "Gm10010" "Tead4" "Tulp3" "Rhno1"
## [12101] "Itfg2" "Fkbp4" "Krtap10-10" "Pzp"
## [12105] "Gm8724" "Clec12b" "Klra5" "Magohb"
## [12109] "Ybx3" "Gm22362" "Tas2r117" "Gm5886"
## [12113] "Gm8956" "Cfap410" "Lrp6" "Dusp16"
## [12117] "Gsg1" "Pbp2" "Ube2q2l" "Gm6728"
## [12121] "Plbd1" "H4c16" "Wbp11" "Mgp"
## [12125] "Dnmt3l" "Erp27" "Arhgdib" "Rerg"
## [12129] "Eps8" "Igbp1b" "Plcz1" "Slco1a4"
## [12133] "Ldhb" "Abcc9" "St8sia1" "Cstb"
## [12137] "C2cd5" "Sox5" "Dnai7" "Kras"
## [12141] "Lmntd1" "Bhlhe41" "Ints13" "Tm7sf3"
## [12145] "Pthlh" "Ergic2" "Gm5951" "Gm55131"
## [12149] "Dennd5b" "Gm10388" "Ndufa3" "Prpf31"
## [12153] "Cnot3" "Tsen34" "Rps9" "Ttyh1"
## [12157] "Leng8" "Ilvbl" "Lilra5" "Atp6v0c-ps2"
## [12161] "Brsk1" "Nat14" "Zfp524" "Zfp865"
## [12165] "Zfp580" "Ccdc106" "U2af2" "Epn1"
## [12169] "Cdc34" "Rps18" "Galp" "Zfp78"
## [12173] "Zfp28" "Zfp264" "Gm6909" "Vmn2r-ps53"
## [12177] "Zfp606" "2900092C05Rik" "Rps5" "Bsg"
## [12181] "Zfp324" "Lig1" "Phf20-ps" "Phf20"
## [12185] "Gm25354" "Zfp541" "Napa" "Slc8a2"
## [12189] "Meis3" "Bbc3" "Fgf22" "Zc3h4"
## [12193] "Tmem160" "n-R5s151" "Ap2s1" "Slc1a5"
## [12197] "Strn4" "Dact3" "Pnma8b" "Pnma8a"
## [12201] "Gm6065" "Rbm42" "Fstl3" "Pglyrp1"
## [12205] "Nova2" "Mypop" "Irf2bp1" "Dmpk"
## [12209] "Mir330" "Gpr4" "Opa3" "Rtn2"
## [12213] "Ercc1" "Palm" "Ppp1r13l" "Ckm"
## [12217] "Exoc3l2" "Zfp296" "Ceacam20" "Nlrp4e"
## [12221] "Nlrp5" "Vmn1r179" "Vmn1r181" "Zfp180"
## [12225] "Misp" "Zfp114" "Zfp108" "Zfp93"
## [12229] "Lypd5" "Zfp428" "Xrcc1" "Phldb3"
## [12233] "Dmrtc2" "Rps19" "Arhgef1" "Ptbp1"
## [12237] "Zfp574" "D930028M14Rik" "Zfp526" "Prr19"
## [12241] "Megf8" "4732471J01Rik" "Gm4607" "Dmac2"
## [12245] "B3gnt8" "Exosc5" "Cfd" "Tgfb1"
## [12249] "Gm55088" "Cyp2f2" "Actmap" "Blvrb"
## [12253] "Sertad3" "Prx" "2310022A10Rik" "Ttc9b"
## [12257] "Zfp626" "Arid3a" "Zfp607a" "Fcgbpl1"
## [12261] "Dyrk1b" "Eid2b" "Paf1" "Ifnl3"
## [12265] "Gm19880" "Sycn" "Sars2" "Map4k1"
## [12269] "Wdr18" "Yif1b" "Ppp1r14a" "Dpf1"
## [12273] "4930432E11Rik" "Zfp84" "Zfp568" "Zfp260"
## [12277] "Zfp382" "Cox7a1" "Polr2i" "Grin3b"
## [12281] "Clip3" "Alkbh6" "Syne4" "Tyrobp"
## [12285] "Arhgap33os" "Hspb6" "Igflr1" "2200002J24Rik"
## [12289] "Gm4883" "Sbsn" "Atp5f1d" "Fam187b"
## [12293] "Gm10640" "Gm12755" "Scgb1b27" "Pepd"
## [12297] "Cebpa" "Rhpn2" "Cep89" "Slc7a9"
## [12301] "B230322F03Rik" "Midn" "Ankrd27" "E130304I02Rik"
## [12305] "1600014C10Rik" "Zfp939" "Ube2h" "Vstm2b"
## [12309] "4930433I11Rik" "Gm4884" "Gm5592" "Gm9246"
## [12313] "Copg1" "Cirbp" "Gm15470" "Zfp141"
## [12317] "Gm19246" "Gm7211" "Gm9266" "Siglecf"
## [12321] "Siglecg" "Lim2" "Nkg7" "Cldnd2"
## [12325] "Fam174c" "Etfb" "Zfp719" "Zfp819"
## [12329] "Ctu1" "Klk14" "Klk12" "Klk10"
## [12333] "Klk4" "Klk15" "Klk1b7-ps" "Pwwp3a"
## [12337] "Klk1b8" "Klk1b1" "Klk1b9" "Klk1b26"
## [12341] "Klk1b27" "Klk1b21" "Klk1b22" "Klk1b24"
## [12345] "Klk1b4" "Klk1b5" "Ndufs7" "Shank1"
## [12349] "Syt3" "Lrrc4b" "Garin5a" "Izumo2"
## [12353] "Vrk3" "Nup62" "Il4i1" "Akt1s1"
## [12357] "Pnkp" "Rps15" "Tsks" "Irf3"
## [12361] "Rras" "Nosip" "Mir150" "Pih1d1"
## [12365] "Slc17a7" "Pth2" "Tead2" "Slc6a16"
## [12369] "Reep6" "Rpl14-ps1" "Ntf5" "Lhb"
## [12373] "Plekha4" "Hsd17b14" "Bcat2" "Izumo1"
## [12377] "Rasip1" "Ntn5" "Car11" "Dot1l"
## [12381] "Dbp" "Fam83e" "Lmtk3" "Kdelr1"
## [12385] "Odad1" "Myod1" "Kcnc1" "Ifitm2"
## [12389] "Ldhc" "Tmem86a" "Sf3a2" "Zdhhc13"
## [12393] "Nav2" "Htatip2" "Prmt3" "4933405O20Rik"
## [12397] "Ano5" "Slc17a6" "Gas2" "Gm6181"
## [12401] "Gm9367" "Oaz1" "Tubgcp5" "Herc2"
## [12405] "Oca2" "Ndn" "Magel2" "Otud7a"
## [12409] "Trpm1" "Mir211" "Mtmr10" "Mcee"
## [12413] "Tmprss9" "Tars3" "Pcsk6" "Snrpa1"
## [12417] "Selenos" "Chsy1" "Lins1" "Cers3"
## [12421] "Adamts17" "Lysmd4" "Igf1r" "Psap"
## [12425] "Gadd45b" "Rgma" "Fam174b" "Gm10161"
## [12429] "Akap13" "Mrps11" "Aen" "Abhd2"
## [12433] "Ticrr" "9330171B17Rik" "Mesp2" "Thop1"
## [12437] "Sema4b" "Ngrn" "Vps33b" "Prc1"
## [12441] "Hddc3" "Zscan2" "Slc28a1" "Whamm"
## [12445] "Sh3gl3" "Efl1" "Map2k2" "Tmc3"
## [12449] "2610206C17Rik" "Vmn2r71" "Grm5" "Ctsc"
## [12453] "Fzd4" "Prss23os" "Picalm" "Sytl2"
## [12457] "Ccdc89" "Zbtb7a" "Crebzf" "Dlg2"
## [12461] "Ccdc90b" "Rab30" "Prcp" "Fam181b"
## [12465] "Gm8309" "Tenm4" "Nars2" "Gab2"
## [12469] "Zfr2" "Alg8" "Ndufc2" "Ints4"
## [12473] "Gm24412" "Rsf1" "Clns1a" "Pak1"
## [12477] "Gdpd4" "Thap12" "Wnt11" "Pip5k1c"
## [12481] "Map6" "Gdpd5" "Gm56176" "Arrb1"
## [12485] "Mir326" "Gm10605" "Xrra1" "C2cd3"
## [12489] "Ucp2" "Coa4" "Cactin" "Rab6a"
## [12493] "Fam168a" "Fchsd2" "Arap1" "Mir139"
## [12497] "Clpb" "Gm10602" "Numa1" "Art1"
## [12501] "Pgap2" "Tbxa2r" "Stim1" "Rrm1"
## [12505] "Or52b3" "Or51r1" "Or52j3" "Or52e3"
## [12509] "Or52ab7" "Usp17lc" "Or52ae7" "Gm15115"
## [12513] "Mfsd12" "Or51k2" "Or51k7" "Or52d1"
## [12517] "Or52e7" "Or52e5" "Smpd1" "Or2ag2b"
## [12521] "Or10a5" "Or2d36" "Nlrp14" "Dohh"
## [12525] "Rbmxl2" "Ppfibp2" "Rbm3" "Gm6007"
## [12529] "Eif3f" "Tub" "Snora3" "Akip1"
## [12533] "Ipo7" "Snora23" NA NA
## [12537] NA NA NA NA
## [12541] NA NA NA NA
## [12545] NA NA NA NA
## [12549] NA NA NA NA
## [12553] NA NA NA NA
## [12557] NA NA NA NA
## [12561] NA NA NA NA
## [12565] NA NA NA NA
## [12569] NA NA NA NA
## [12573] NA NA NA NA
## [12577] NA NA NA NA
## [12581] NA NA NA NA
## [12585] NAgene_ranks <- sort(gene_ranks[!is.na(names(gene_ranks))], decreasing = TRUE)
top_n <- 30
for (cat in categories) {
gmt_file <- sprintf("../m5.go.%s.v2024.1.Mm.symbols.gmt", tolower(cat))
if (file.exists(gmt_file)) {
pathways <- gmtPathways(gmt_file)
fgseaRes <- fgsea(pathways = pathways, stats = gene_ranks, minSize = 15, maxSize = 500)
fgseaRes <- fgseaRes[order(fgseaRes$padj), ]
fgseaRes$leadingEdge <- sapply(fgseaRes$leadingEdge, paste, collapse = "; ")
write.csv(fgseaRes, sprintf("results/tables/fgsea_new_GO_%s.csv", cat), row.names = FALSE)
fgsea_top <- head(fgseaRes, top_n)
p_bubble <- ggplot(fgsea_top, aes(x = NES, y = reorder(pathway, NES), size = size, color = padj)) +
geom_point() +
scale_color_gradient(low = "red", high = "blue", name = "FDR") +
scale_size(range = c(3, 10)) +
labs(title = sprintf("Bubble Plot - Top Enriched Pathways (GO:%s)", cat), x = "NES", y = "Pathway") +
theme_minimal(base_size = 12)
print(p_bubble)
} else {
warning(sprintf("Plik %s nie znaleziony. Pomijam fgsea dla GO:%s.", gmt_file, cat))
}
}## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.01% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.01% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.01% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
gProfiler Analysis
if (length(de_genes) > 0) {
gp <- gost(query = de_genes,
organism = "mmusculus",
sources = c("GO:BP", "GO:CC", "GO:MF", "KEGG", "REAC"),
correction_method = "fdr",
user_threshold = 0.05)
gp_result_fixed <- gp$result
list_cols <- sapply(gp_result_fixed, is.list)
gp_result_fixed[list_cols] <- lapply(gp_result_fixed[list_cols], function(col) sapply(col, paste, collapse = "; "))
if (!dir.exists("results/tables/")) dir.create("results/tables/", recursive = TRUE)
if (!dir.exists("results/plots/")) dir.create("results/plots/", recursive = TRUE)
write.csv(gp_result_fixed, "results/tables/gprofiler_enrichment_full.csv", row.names = FALSE)
top_n <- 30
sources <- c("GO:BP", "GO:CC", "GO:MF", "KEGG", "REAC")
for (src in sources) {
gp_src <- subset(gp_result_fixed, source == src)
if (nrow(gp_src) > 0) {
gp_top <- head(gp_src[order(gp_src$p_value), ], top_n)
safe_src <- gsub("[:]", "_", src)
write.csv(gp_src, sprintf("results/tables/gprofiler_%s_results_new.csv", safe_src), row.names = FALSE)
p_bubble <- ggplot(gp_top, aes(x = -log10(p_value), y = reorder(term_name, -log10(p_value)),
size = intersection_size, color = p_value)) +
geom_point() +
scale_color_gradient(low = "red", high = "blue", name = "p-value") +
scale_size(range = c(3, 10), name = "Intersection Size") +
labs(title = paste("gProfiler Bubble Plot -", src),
x = "-log10(p-value)", y = "Term") +
theme_minimal(base_size = 12)
print(p_bubble)
}
}
} else {
warning("Brak genów DE do analizy gProfiler.")
}
TopGO Analysis
gene_universe <- unique(na.omit(final_combined_unique$SYMBOL_final))
geneList <- factor(as.integer(gene_universe %in% de_genes))
names(geneList) <- gene_universe
ontologies <- c("BP", "MF", "CC")
top_n <- 30
for (ont in ontologies) {
GOdata <- new("topGOdata",
ontology = ont,
allGenes = geneList,
annot = annFUN.org,
mapping = "org.Mm.eg.db",
ID = "symbol")
resultFisher <- runTest(GOdata, algorithm = "elim", statistic = "fisher")
topgo_table <- GenTable(GOdata, Fisher.elim = resultFisher, topNodes = top_n)
topgo_table$Fisher.elim <- as.numeric(sub("<", "", topgo_table$Fisher.elim))
topgo_table$Fisher.elim[is.na(topgo_table$Fisher.elim)] <- 1 #' dla wartości "<1e-30"
write.csv(topgo_table, sprintf("results/tables/topGO_%s_results_new.csv", ont), row.names = FALSE)
p_bubble <- ggplot(topgo_table, aes(x = -log10(Fisher.elim), y = reorder(Term, -log10(Fisher.elim)),
size = Significant, color = Fisher.elim)) +
geom_point() +
scale_color_gradient(low = "red", high = "blue", name = "p-value") +
scale_size(range = c(3, 10), name = "Significant Genes") +
labs(title = paste("topGO:", ont, "- Bubble Plot"), x = "-log10(p-value)", y = "GO Term") +
theme_minimal(base_size = 12)
print(p_bubble)
pdf(sprintf("results/plots/topGO_GOgraph_%s.pdf", ont), width = 8, height = 10)
showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 10, useInfo = "all")
dev.off()
}##
## Building most specific GOs .....## ( 10785 GO terms found. )##
## Build GO DAG topology ..........## ( 13945 GO terms and 30776 relations. )##
## Annotating nodes ...............## ( 11060 genes annotated to the GO terms. )##
## -- Elim Algorithm --
##
## the algorithm is scoring 2236 nontrivial nodes
## parameters:
## test statistic: fisher
## cutOff: 0.01##
## Level 16: 2 nodes to be scored (0 eliminated genes)##
## Level 15: 6 nodes to be scored (0 eliminated genes)##
## Level 14: 19 nodes to be scored (0 eliminated genes)##
## Level 13: 31 nodes to be scored (0 eliminated genes)##
## Level 12: 72 nodes to be scored (11 eliminated genes)##
## Level 11: 122 nodes to be scored (20 eliminated genes)##
## Level 10: 200 nodes to be scored (48 eliminated genes)##
## Level 9: 270 nodes to be scored (57 eliminated genes)##
## Level 8: 311 nodes to be scored (65 eliminated genes)##
## Level 7: 331 nodes to be scored (87 eliminated genes)##
## Level 6: 359 nodes to be scored (112 eliminated genes)##
## Level 5: 279 nodes to be scored (604 eliminated genes)##
## Level 4: 163 nodes to be scored (669 eliminated genes)##
## Level 3: 57 nodes to be scored (669 eliminated genes)##
## Level 2: 13 nodes to be scored (669 eliminated genes)##
## Level 1: 1 nodes to be scored (669 eliminated genes)
##
## Building most specific GOs .....## ( 3832 GO terms found. )##
## Build GO DAG topology ..........## ( 4304 GO terms and 5602 relations. )##
## Annotating nodes ...............## ( 10907 genes annotated to the GO terms. )##
## -- Elim Algorithm --
##
## the algorithm is scoring 557 nontrivial nodes
## parameters:
## test statistic: fisher
## cutOff: 0.01##
## Level 12: 1 nodes to be scored (0 eliminated genes)##
## Level 11: 2 nodes to be scored (0 eliminated genes)##
## Level 10: 7 nodes to be scored (0 eliminated genes)##
## Level 9: 37 nodes to be scored (0 eliminated genes)##
## Level 8: 64 nodes to be scored (0 eliminated genes)##
## Level 7: 88 nodes to be scored (0 eliminated genes)##
## Level 6: 101 nodes to be scored (88 eliminated genes)##
## Level 5: 109 nodes to be scored (134 eliminated genes)##
## Level 4: 96 nodes to be scored (146 eliminated genes)##
## Level 3: 40 nodes to be scored (207 eliminated genes)##
## Level 2: 11 nodes to be scored (207 eliminated genes)##
## Level 1: 1 nodes to be scored (207 eliminated genes)
##
## Building most specific GOs .....## ( 1667 GO terms found. )##
## Build GO DAG topology ..........## ( 1830 GO terms and 2984 relations. )##
## Annotating nodes ...............## ( 11109 genes annotated to the GO terms. )##
## -- Elim Algorithm --
##
## the algorithm is scoring 338 nontrivial nodes
## parameters:
## test statistic: fisher
## cutOff: 0.01##
## Level 11: 7 nodes to be scored (0 eliminated genes)##
## Level 10: 26 nodes to be scored (0 eliminated genes)##
## Level 9: 43 nodes to be scored (14 eliminated genes)##
## Level 8: 48 nodes to be scored (14 eliminated genes)##
## Level 7: 48 nodes to be scored (14 eliminated genes)##
## Level 6: 60 nodes to be scored (14 eliminated genes)##
## Level 5: 46 nodes to be scored (14 eliminated genes)##
## Level 4: 26 nodes to be scored (14 eliminated genes)##
## Level 3: 31 nodes to be scored (786 eliminated genes)##
## Level 2: 2 nodes to be scored (786 eliminated genes)##
## Level 1: 1 nodes to be scored (786 eliminated genes)
####################